Research workbench
Structure of the major type 1 pilus subunit fima bound to the fimc chaperone
Analyse Structure of the major type 1 pilus subunit fima bound to the fimc chaperone in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SQB
- Type
- protein
- Length
- 1,100 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chaperone protein fimc; Type-1 fimbrial protein, a chain
- UniProt
- P31697, P04128
- Pockets
- 16 · best druggability 0.71
Structure
x-ray diffraction · 7 distinct chains · 4% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chaperone protein fimc | protein | 191 | 3% helix, 52% strand | P31697 |
| B, D | Type-1 fimbrial protein, a chain | protein | 145 | 8% helix, 46% strand | P04128 |
| C | Chaperone protein fimc | protein | 200 | 3% helix, 54% strand | P31697 |
| E | Chaperone protein fimc | protein | 176 | 3% helix, 45% strand | P31697 |
| F | Type-1 fimbrial protein, a chain | protein | 89 | 7% helix, 43% strand | P04128 |
| G | Chaperone protein fimc | protein | 76 | 0% helix, 64% strand | P31697 |
| H | Type-1 fimbrial protein, a chain | protein | 78 | 0% helix, 38% strand | P04128 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains C, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 567 | 0.71 | 0.80 | 88 | empty |
| 2 | 360 | 0.69 | 0.82 | 42 | empty |
| 3 | 137 | 0.68 | 0.89 | 36 | empty |
| 4 | 64 | 0.67 | 0.94 | 22 | empty |
| 5 | 534 | 0.61 | 0.74 | 47 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1796 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 1718 Ų buried · 37 hydrogen bonds · protein-protein
- E–F · 1339 Ų buried · 28 hydrogen bonds · protein-protein
- G–H · 696 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 473 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3SQB · Structure of the major type 1 pilus subunit FimA bound to the FimC chaperone · the same entry in another collection · chain H against H, TM-score 1.00
- P31697 · AlphaFold monomer V2.0 prediction for chaperone protein fimc (P31697) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P31697
- Every structure of UniProt P04128
- Elsewhere: RCSB PDB 3SQB · PDBe 3SQB · UniProt P31697 · UniProt P04128
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