Research workbench
Crystal structure of the fimd usher traversed by the pilus tip complex assembly composed of FIMC:FIMF:FIMG:FIMH
Analyse Crystal structure of the fimd usher traversed by the pilus tip complex assembly… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J3O
- Type
- protein
- Length
- 1,554 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein fimg; Protein fimh; Chaperone protein fimc; Protein fimf; Outer membrane usher…
- UniProt
- P08190, P08191, P31697, P08189, P30130
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 3% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Protein fimg | protein | 144 | 0% helix, 51% strand | P08190 |
| H | Protein fimh | protein | 279 | 2% helix, 47% strand | P08191 |
| C | Chaperone protein fimc | protein | 199 | 2% helix, 51% strand | P31697 |
| F | Protein fimf | protein | 154 | 3% helix, 46% strand | P08189 |
| D | Outer membrane usher protein fimd | protein | 778 | 4% helix, 53% strand | P30130 |
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 619 | 0.84 | 0.89 | 80 | empty |
| 2 | 850 | 0.82 | 0.84 | 121 | empty |
| 3 | 433 | 0.79 | 0.87 | 64 | empty |
| 4 | 228 | 0.71 | 0.87 | 39 | empty |
| 5 | 115 | 0.65 | 0.88 | 24 | empty |
Interfaces
8 interfaces between chains.
- G–D · 2450 Ų buried · 21 hydrogen bonds · protein-protein
- C–F · 1503 Ų buried · 27 hydrogen bonds · protein-protein
- G–F · 1460 Ų buried · 32 hydrogen bonds · protein-protein
- G–H · 1336 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1041 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4J3O · Crystal structure of the FimD usher traversed by the pilus tip complex assembly composed… · the same entry in another collection · chain D against D, TM-score 1.00
- P31697 · AlphaFold monomer V2.0 prediction for chaperone protein fimc (P31697) · a predicted model of the same protein · chain C against A, TM-score 0.98
- P30130 · AlphaFold monomer V2.0 prediction for outer membrane usher protein fimd (P30130) · a predicted model of the same protein · chain D against A, TM-score 0.98
- P08191 · AlphaFold monomer V2.0 prediction for type 1 fimbrin D-mannose specific adhesin (P08191) · a predicted model of the same protein · chain H against A, TM-score 0.96
- P08190 · AlphaFold monomer V2.0 prediction for protein fimg (P08190) · a predicted model of the same protein · chain G against A, TM-score 0.91
- P08189 · AlphaFold monomer V2.0 prediction for protein fimf (P08189) · a predicted model of the same protein · chain F against A, TM-score 0.84
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P08190
- Every structure of UniProt P08191
- Every structure of UniProt P31697
- Every structure of UniProt P08189
- Every structure of UniProt P30130
- Elsewhere: RCSB PDB 4J3O · PDBe 4J3O · UniProt P08190 · UniProt P08191 · UniProt P31697 · UniProt P08189 · UniProt P30130
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