Alpha&ESM hFolds

A database for the comparison of structural models predicted by ESMFold and AlphaFold2 for human proteins.
Now updated with Quality Assessment and Functional characterization of the models.
Part of the Bioinformatics Sweeties collection.

Protein information Download JSON
Protein name NACHT, LRR and PYD domains-containing protein 3
Gene name NLRP3
UniProt accession Q96P20
Sequence length 1036
Protein source SwissProt (reviewed)
Signal/Transit peptide Absent
Highest-coverage PDB Chain 7pzc_A
PDB Chain coverage 0.97
Experimental method (Resolution) Electron Microscopy (3.9 Å)

Sequence alignment (from structure superimposition) Download FASTA

Model Confidence: Very high (pLDDT ≥ 90) High (90 > pLDDT ≥ 70) Low (70 > pLDDT ≥ 50) Very low (pLDDT < 50)

Structure superimposition
ESMFold
AlphaFold2
Structure alignment scores
TM-score 0.58
RMSD 4.25 Å
GDT 0.42
TM-score pLDDT≥50 0.61
TM-score pLDDT≥70 0.62
TM-score pLDDT≥90 0.71
Sequence coverage
ESMFold start - end 161 - 1036
AlphaFold2 start - end 170 - 1036
Alignment length 1080
Match positions 567
Mismatch positions 96
Gap positions (Gap opens) 373 (18)
Self-assessment ESMFold AlphaFold2
Mean pLDDT 84.26 81.56
External validation ESMFold AlphaFold2
DeepAccNet mean pLDDT 84.93 91.88
QMEANDisCo mean pLDDT 68.1 70.9
QATEN mean pLDDT 67.5 67.61

AlphaFold is better than ESMFold according to 3/3 external QA tools

 Name Type Start End TM-score ESMFold
pLDDT 		AlphaFold2
pLDDT
PYRIN Domain 10 85 0.99 85.97 86.23
FISNA Family 140 210 0.75 72.09 76.7
NACHT Domain 220 389 0.98 90.26 87.39
NOD2_WH Domain 466 520 0.83 88.16 76.89
NLRC4_HD2 Domain 522 644 0.93 82.79 79.38
LRR_6 Repeat 740 762 0.97 85.27 91.24
LRR_6 Repeat 796 819 0.99 95.39 97.04
LRR_6 Repeat 854 873 0.99 96.8 96.74
LRR_6 Repeat 910 933 0.99 97.37 97.08
LRR_6 Repeat 968 990 0.98 95.4 95.23
Position Wild type Mutated type Description
21 D H KEFH; does not affect ability to homooligomerize into ordered polymers (from: UniProt); dbSNP:rs200154873
174 I T CINCA (from: UniProt); dbSNP:rs180177449
200 V M FCAS1 and MWS (from: UniProt); dbSNP:rs121908147
262 R L CINCA (from: UniProt); dbSNP:rs180177442
262 R P CINCA (from: UniProt); dbSNP:rs180177442
262 R W FCAS1 and MWS; spontaneous polymerization into inflammasome speck (from: UniProt); dbSNP:rs121908150
266 L H CINCA (from: UniProt); dbSNP:rs180177436
305 D G CINCA (from: UniProt); dbSNP:rs180177447
305 D N CINCA and MWS; spontaneous polymerization into inflammasome speck (from: UniProt); dbSNP:rs121908153
307 L P FCAS1 and MWS (from: UniProt); dbSNP:rs180177431
308 Q K CINCA (from: UniProt); dbSNP:rs180177432
311 F S CINCA (from: UniProt); dbSNP:rs121908154
350 T M MWS and CINCA; spontaneous polymerization into inflammasome speck (from: UniProt); dbSNP:rs151344629
354 A V MWS (from: UniProt); dbSNP:rs121908149
355 L P FCAS1 (from: UniProt); dbSNP:rs28937896
356 E D CINCA (from: UniProt); dbSNP:rs180177444
360 H R CINCA (from: UniProt); dbSNP:rs180177434
407 T P CINCA (from: UniProt); dbSNP:rs180177445
438 T I CINCA (from: UniProt); dbSNP:rs180177433
438 T N CINCA (from: UniProt); dbSNP:rs180177433
441 A T MWS (from: UniProt); dbSNP:rs180177430
441 A V FCAS1 (from: UniProt); dbSNP:rs121908146
490 R K FCAS1 (from: UniProt); dbSNP:rs145268073
525 F C FCAS1 (from: UniProt); dbSNP:rs180177478
525 F L CINCA (from: UniProt); dbSNP:rs180177439
571 G R MWS (from: UniProt); dbSNP:rs121908151
572 Y C CINCA (from: UniProt); dbSNP:rs180177438
575 F S CINCA (from: UniProt); dbSNP:rs121908152
629 E G FCAS1 (from: UniProt); dbSNP:rs121908148
634 L F CINCA (from: UniProt); dbSNP:rs180177446
664 M T CINCA (from: UniProt); dbSNP:rs180177435
861 Y C CINCA (from: UniProt); dbSNP:rs180177452

Sequence alignment (from structure superimposition) Download FASTA

Model Confidence: Very high (pLDDT ≥ 90) High (90 > pLDDT ≥ 70) Low (70 > pLDDT ≥ 50) Very low (pLDDT < 50)

Structure superimposition
ESMFold
PDB (7pzc_A)
Structure alignment scores
TM-score 0.73
RMSD 4.74 Å
TM-score pLDDT≥50 0.75
TM-score pLDDT≥70 0.77
TM-score pLDDT≥90 0.76
Sequence coverage
ESMFold start - end 94 - 1034
PDB start - end 99 - 1008
Alignment length 976
Match positions 782
Mismatch positions 93
ESMFold gap positions 135
PDB gap positions 161
Gap opens 21

Sequence alignment (from structure superimposition) Download FASTA

Model Confidence: Very high (pLDDT ≥ 90) High (90 > pLDDT ≥ 70) Low (70 > pLDDT ≥ 50) Very low (pLDDT < 50)

Structure superimposition
AlphaFold2
PDB (7pzc_A)
Structure alignment scores
TM-score 0.57
RMSD 4.51 Å
TM-score pLDDT≥50 0.6
TM-score pLDDT≥70 0.61
TM-score pLDDT≥90 0.69
Sequence coverage
AlphaFold2 start - end 168 - 1036
PDB start - end 151 - 1010
Alignment length 1077
Match positions 559
Mismatch positions 93
AlphaFold2 gap positions 358
PDB gap positions 384
Gap opens 20