Research workbench
Crystal structure of the ternary complex of fimd (N-terminal domain, fimdn) with fimc and the N-terminally truncated pilus subunit fimf (fimft)
Analyse Crystal structure of the ternary complex of fimd (N-terminal domain, fimdn)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BWU
- Type
- protein
- Length
- 449 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chaperone protein fimc; Outer membrane usher protein fimd, N-terminal domain; Protein fimf
- UniProt
- P31697, P30130, P08189
- Pockets
- 7 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Chaperone protein fimc | protein | 200 | 3% helix, 55% strand | P31697 |
| D | Outer membrane usher protein fimd, N-terminal domain | protein | 121 | 26% helix, 30% strand | P30130 |
| F | Protein fimf | protein | 128 | 2% helix, 49% strand | P08189 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 13 copies · chains C, D, F
- PEG · Di(hydroxyethyl)ether · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.52 | 0.84 | 22 | EDO |
| 2 | 190 | 0.49 | 0.76 | 35 | EDO |
| 3 | 124 | 0.42 | 0.76 | 25 | EDO |
| 4 | 102 | 0.41 | 0.77 | 24 | empty |
| 5 | 110 | 0.40 | 0.75 | 19 | empty |
Interfaces
3 interfaces between chains.
- C–F · 1449 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 1023 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 136 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3BWU · Crystal structure of the ternary complex of FimD (N-Terminal Domain, FimDN) with FimC and… · the same entry in another collection · chain C against C, 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 0.99
- P08189 · AlphaFold monomer V2.0 prediction for protein fimf (P08189) · a predicted model of the same protein · chain F against A, TM-score 0.94
- 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 0.86
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 P30130
- Every structure of UniProt P08189
- Elsewhere: RCSB PDB 3BWU · PDBe 3BWU · UniProt P31697 · UniProt P30130 · UniProt P08189
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