Project name: e6wt

Status: done

Started: 2025-02-06 04:17:59
Settings
Chain sequence(s) B: MTEQQWNFAGIEAAASAIQGNVTSIHSLLDEGKQSLTKLAAAWGGSGSEAYQGVQQKWDATATELNNALQNLARTISEAGQAMASTEGNVTGMFA
input PDB
Selected Chain(s) B
Distance of aggregation 10 Å
FoldX usage Yes
Dynamic mode No
Automated mutations Yes
Downloads Download all the data
Simulation log 
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:00)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:00)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with B chain(s) selected             (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:00)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:00:44)
[INFO]       Auto_mut: Residue number 694 from chain B and a score of 1.715 omitted from automated 
                       muatation (excluded by the user).                                           (00:00:45)
[INFO]       Auto_mut: Residue number 608 from chain B and a score of 1.204 (phenylalanine)        
                       selected for automated muatation                                            (00:00:45)
[INFO]       Auto_mut: Residue number 693 from chain B and a score of 1.199 (methionine) selected  
                       for automated muatation                                                     (00:00:45)
[INFO]       Auto_mut: Residue number 695 from chain B and a score of 0.912 omitted from automated 
                       muatation (excluded by the user).                                           (00:00:45)
[INFO]       Auto_mut: Residue number 611 from chain B and a score of 0.560 (isoleucine) selected  
                       for automated muatation                                                     (00:00:45)
[INFO]       Auto_mut: Residue number 609 from chain B and a score of 0.474 (alanine) selected for 
                       automated muatation                                                         (00:00:45)
[INFO]       Auto_mut: Residue number 691 from chain B and a score of 0.362 (threonine) selected   
                       for automated muatation                                                     (00:00:45)
[INFO]       Auto_mut: Residue number 642 from chain B and a score of 0.158 (alanine) selected for 
                       automated muatation                                                         (00:00:45)
[INFO]       Auto_mut: Mutating residue number 693 from chain B (methionine) into glutamic acid    (00:00:45)
[INFO]       Auto_mut: Mutating residue number 608 from chain B (phenylalanine) into aspartic acid 
                       Mutating residue number 608 from chain B (phenylalanine) into aspartic acid (00:00:45)
[INFO]       Auto_mut: Mutating residue number 608 from chain B (phenylalanine) into glutamic acid 
                       Mutating residue number 608 from chain B (phenylalanine) into glutamic acid (00:00:45)
[INFO]       Auto_mut: Mutating residue number 608 from chain B (phenylalanine) into arginine      (00:01:10)
[INFO]       Auto_mut: Mutating residue number 693 from chain B (methionine) into lysine           (00:01:10)
[INFO]       Auto_mut: Mutating residue number 608 from chain B (phenylalanine) into lysine        (00:01:12)
[INFO]       Auto_mut: Mutating residue number 693 from chain B (methionine) into aspartic acid    (00:01:43)
[INFO]       Auto_mut: Mutating residue number 611 from chain B (isoleucine) into glutamic acid    (00:01:44)
[INFO]       Auto_mut: Mutating residue number 611 from chain B (isoleucine) into aspartic acid    (00:01:44)
[INFO]       Auto_mut: Mutating residue number 693 from chain B (methionine) into arginine         (00:02:08)
[INFO]       Auto_mut: Mutating residue number 611 from chain B (isoleucine) into arginine         (00:02:08)
[INFO]       Auto_mut: Mutating residue number 611 from chain B (isoleucine) into lysine           (00:02:11)
[INFO]       Auto_mut: Mutating residue number 609 from chain B (alanine) into glutamic acid       (00:02:36)
[INFO]       Auto_mut: Mutating residue number 609 from chain B (alanine) into aspartic acid       (00:02:39)
[INFO]       Auto_mut: Mutating residue number 691 from chain B (threonine) into glutamic acid     (00:02:49)
[INFO]       Auto_mut: Mutating residue number 609 from chain B (alanine) into lysine              (00:03:02)
[INFO]       Auto_mut: Mutating residue number 609 from chain B (alanine) into arginine            (00:03:04)
[INFO]       Auto_mut: Mutating residue number 691 from chain B (threonine) into lysine            (00:03:17)
[INFO]       Auto_mut: Mutating residue number 691 from chain B (threonine) into aspartic acid     (00:03:34)
[INFO]       Auto_mut: Mutating residue number 642 from chain B (alanine) into glutamic acid       (00:03:34)
[INFO]       Auto_mut: Mutating residue number 642 from chain B (alanine) into aspartic acid       (00:03:48)
[INFO]       Auto_mut: Mutating residue number 642 from chain B (alanine) into lysine              (00:03:58)
[INFO]       Auto_mut: Mutating residue number 691 from chain B (threonine) into arginine          (00:04:00)
[INFO]       Auto_mut: Mutating residue number 642 from chain B (alanine) into arginine            (00:04:13)
[INFO]       Auto_mut: Effect of mutation residue number 608 from chain B (phenylalanine) into     
                       glutamic acid: Energy difference: -0.1424 kcal/mol, Difference in average   
                       score from the base case: -0.1453                                           (00:04:40)
[INFO]       Auto_mut: Effect of mutation residue number 608 from chain B (phenylalanine) into     
                       lysine: Energy difference: -0.0153 kcal/mol, Difference in average score    
                       from the base case: -0.1409                                                 (00:04:40)
[INFO]       Auto_mut: Effect of mutation residue number 608 from chain B (phenylalanine) into     
                       aspartic acid: Energy difference: 0.6789 kcal/mol, Difference in average    
                       score from the base case: -0.1625                                           (00:04:40)
[INFO]       Auto_mut: Effect of mutation residue number 608 from chain B (phenylalanine) into     
                       arginine: Energy difference: -0.0532 kcal/mol, Difference in average score  
                       from the base case: -0.1348                                                 (00:04:40)
[INFO]       Auto_mut: Effect of mutation residue number 693 from chain B (methionine) into        
                       glutamic acid: Energy difference: -0.4707 kcal/mol, Difference in average   
                       score from the base case: -0.0821                                           (00:04:40)
[INFO]       Auto_mut: Effect of mutation residue number 693 from chain B (methionine) into        
                       lysine: Energy difference: -0.6427 kcal/mol, Difference in average score    
                       from the base case: -0.0881                                                 (00:04:40)
[INFO]       Auto_mut: Effect of mutation residue number 693 from chain B (methionine) into        
                       aspartic acid: Energy difference: -0.4792 kcal/mol, Difference in average   
                       score from the base case: -0.0786                                           (00:04:40)
[INFO]       Auto_mut: Effect of mutation residue number 693 from chain B (methionine) into        
                       arginine: Energy difference: -0.5436 kcal/mol, Difference in average score  
                       from the base case: -0.0780                                                 (00:04:40)
[INFO]       Auto_mut: Effect of mutation residue number 611 from chain B (isoleucine) into        
                       glutamic acid: Energy difference: 0.6782 kcal/mol, Difference in average    
                       score from the base case: -0.0893                                           (00:04:40)
[INFO]       Auto_mut: Effect of mutation residue number 611 from chain B (isoleucine) into        
                       lysine: Energy difference: -0.0101 kcal/mol, Difference in average score    
                       from the base case: -0.0646                                                 (00:04:40)
[INFO]       Auto_mut: Effect of mutation residue number 611 from chain B (isoleucine) into        
                       aspartic acid: Energy difference: 0.8368 kcal/mol, Difference in average    
                       score from the base case: -0.0945                                           (00:04:40)
[INFO]       Auto_mut: Effect of mutation residue number 611 from chain B (isoleucine) into        
                       arginine: Energy difference: -0.6842 kcal/mol, Difference in average score  
                       from the base case: -0.0814                                                 (00:04:40)
[INFO]       Auto_mut: Effect of mutation residue number 609 from chain B (alanine) into glutamic  
                       acid: Energy difference: -0.9443 kcal/mol, Difference in average score from 
                       the base case: -0.0369                                                      (00:04:40)
[INFO]       Auto_mut: Effect of mutation residue number 609 from chain B (alanine) into lysine:   
                       Energy difference: -0.4975 kcal/mol, Difference in average score from the   
                       base case: -0.0527                                                          (00:04:40)
[INFO]       Auto_mut: Effect of mutation residue number 609 from chain B (alanine) into aspartic  
                       acid: Energy difference: -0.7868 kcal/mol, Difference in average score from 
                       the base case: -0.0572                                                      (00:04:40)
[INFO]       Auto_mut: Effect of mutation residue number 609 from chain B (alanine) into arginine: 
                       Energy difference: -0.9033 kcal/mol, Difference in average score from the   
                       base case: -0.0286                                                          (00:04:40)
[INFO]       Auto_mut: Effect of mutation residue number 691 from chain B (threonine) into         
                       glutamic acid: Energy difference: 1.3406 kcal/mol, Difference in average    
                       score from the base case: -0.0194                                           (00:04:40)
[INFO]       Auto_mut: Effect of mutation residue number 691 from chain B (threonine) into lysine: 
                       Energy difference: 0.4384 kcal/mol, Difference in average score from the    
                       base case: 0.0266                                                           (00:04:40)
[INFO]       Auto_mut: Effect of mutation residue number 691 from chain B (threonine) into         
                       aspartic acid: Energy difference: 2.2284 kcal/mol, Difference in average    
                       score from the base case: 0.0133                                            (00:04:40)
[INFO]       Auto_mut: Effect of mutation residue number 691 from chain B (threonine) into         
                       arginine: Energy difference: 0.3589 kcal/mol, Difference in average score   
                       from the base case: -0.0030                                                 (00:04:40)
[INFO]       Auto_mut: Effect of mutation residue number 642 from chain B (alanine) into glutamic  
                       acid: Energy difference: -0.0462 kcal/mol, Difference in average score from 
                       the base case: -0.0819                                                      (00:04:40)
[INFO]       Auto_mut: Effect of mutation residue number 642 from chain B (alanine) into lysine:   
                       Energy difference: -0.1753 kcal/mol, Difference in average score from the   
                       base case: -0.0721                                                          (00:04:40)
[INFO]       Auto_mut: Effect of mutation residue number 642 from chain B (alanine) into aspartic  
                       acid: Energy difference: 0.1620 kcal/mol, Difference in average score from  
                       the base case: -0.0619                                                      (00:04:40)
[INFO]       Auto_mut: Effect of mutation residue number 642 from chain B (alanine) into arginine: 
                       Energy difference: -0.1171 kcal/mol, Difference in average score from the   
                       base case: -0.0810                                                          (00:04:40)
[INFO]       Main:     Simulation completed successfully.                                          (00:04:44)
Show buried residues
Minimal score value
-3.1242
Maximal score value
1.715
Average score
-1.0338
Total score value
-98.2138
Download the table (csv)

The table below lists A3D score for protein residues. Residues with A3D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan3D score mutation
residue index residue name chain Aggrescan3D score
mutation
601 M B -0.2152
602 T B -1.0066
603 E B -2.4566
604 Q B -2.1540
605 Q B -1.7215
606 W B -0.1768
607 N B -0.5420
608 F B 1.2044
609 A B 0.4742
610 G B -0.0170
611 I B 0.5596
612 E B -0.5828
613 A B -0.4106
614 A B 0.0213
615 A B 0.0000
616 S B -0.9621
617 A B -0.6678
618 I B -0.7746
619 Q B -1.4940
620 G B -1.4297
621 N B -1.7261
622 V B 0.0000
623 T B -1.0989
624 S B -1.0423
625 I B -0.6198
626 H B -1.6591
627 S B -1.2523
628 L B -0.7532
629 L B -1.4875
630 D B -3.1242
631 E B -2.9406
632 G B -1.9098
633 K B -2.5468
634 Q B -2.7073
635 S B -1.8578
636 L B 0.0000
637 T B -1.2438
638 K B -1.7289
639 L B -0.1640
640 A B 0.0000
641 A B -0.2246
642 A B 0.1580
643 W B 0.0101
644 G B -0.4936
645 G B -0.9085
646 S B -1.1450
647 G B -1.2610
648 S B -1.5341
649 E B -2.3600
650 A B -1.2324
651 Y B -1.2288
652 Q B -2.3393
653 G B -1.7539
654 V B -1.4732
655 Q B -2.1423
656 Q B -2.6863
657 K B -2.6871
658 W B -2.0119
659 D B -2.5673
660 A B -1.9475
661 T B -1.4982
662 A B 0.0000
663 T B -1.5623
664 E B -2.0414
665 L B -0.6077
666 N B -1.5367
667 N B -2.5061
668 A B -1.4535
669 L B 0.0000
670 Q B -2.7953
671 N B -2.2229
672 L B -0.7637
673 A B 0.0000
674 R B -2.2452
675 T B -0.9239
676 I B -0.4558
677 S B -1.1499
678 E B -1.0105
679 A B -0.5958
680 G B -1.1517
681 Q B -1.4964
682 A B 0.0000
683 M B -0.3487
684 A B -0.7486
685 S B -0.8731
686 T B -1.1176
687 E B -1.8540
688 G B -0.8170
689 N B -0.5398
690 V B -0.0552
691 T B 0.3616
692 G B 0.0122
693 M B 1.1990
694 F B 1.7150
695 A B 0.9123
Download PDB file
View in 3Dmol
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Automated mutations analysis

In the automated mutations mode, the server selects aggregation prone resides and each selected residue is mutated to glutamic acid, lysine, aspartic acid and arginine. The table below shows 2 best scored mutants for each mutated residue. Protein variants are ordered according to the mutation effect they had on protein stability (energetic effect) together with the difference in the average per-residue aggregation score between the wild type and the mutant (in the table green values indicate a positive change, grey are neutral, and orange/red mean destabilizing or more aggregation prone mutants).
Summary for all the mutants can be found in this CSV file.

Mutant
Energetic effect
Score comparison
MK693B -0.6427 -0.0881 View CSV PDB
IR611B -0.6842 -0.0814 View CSV PDB
FE608B -0.1424 -0.1453 View CSV PDB
MR693B -0.5436 -0.078 View CSV PDB
FR608B -0.0532 -0.1348 View CSV PDB
AD609B -0.7868 -0.0572 View CSV PDB
AE609B -0.9443 -0.0369 View CSV PDB
AR642B -0.1171 -0.081 View CSV PDB
AK642B -0.1753 -0.0721 View CSV PDB
IK611B -0.0101 -0.0646 View CSV PDB
TE691B 1.3406 -0.0194 View CSV PDB
TR691B 0.3589 -0.003 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018