Research workbench
Handover mechanism of the growing pilus by the bacterial outer membrane usher fimd
Analyse Handover mechanism of the growing pilus by the bacterial outer membrane usher… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E15
- Type
- protein
- Length
- 1,554 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chaperone protein fimc; Fimbrial biogenesis outer membrane usher protein; Protein fimf…
- UniProt
- P31697, A0A0F3W955, P08189, P08190, P08191
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 5 distinct chains · 3% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Chaperone protein fimc | protein | 199 | 2% helix, 48% strand | P31697 |
| D | Fimbrial biogenesis outer membrane usher protein | protein | 778 | 5% helix, 53% strand | A0A0F3W955 |
| F | Protein fimf | protein | 154 | 5% helix, 35% strand | P08189 |
| G | Protein fimg | protein | 144 | 0% helix, 46% strand | P08190 |
| H | Type 1 fimbrin D-mannose specific adhesin | protein | 279 | 2% helix, 47% strand | P08191 |
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 719 | 0.85 | 0.89 | 110 | empty |
| 2 | 412 | 0.84 | 0.92 | 74 | empty |
| 3 | 479 | 0.83 | 0.90 | 105 | empty |
| 4 | 347 | 0.79 | 0.89 | 66 | empty |
| 5 | 324 | 0.79 | 0.89 | 55 | empty |
Interfaces
8 interfaces between chains.
- F–G · 1351 Ų buried · 33 hydrogen bonds · protein-protein
- D–G · 1281 Ų buried · 8 hydrogen bonds · protein-protein
- C–F · 1257 Ų buried · 22 hydrogen bonds · protein-protein
- G–H · 1209 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 680 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6E15 · Handover mechanism of the growing pilus by the bacterial outer membrane usher FimD · the same entry in another collection · chain H against H, TM-score 1.00
- 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
- P31697 · AlphaFold monomer V2.0 prediction for chaperone protein fimc (P31697) · a predicted model of the same protein · chain C against A, TM-score 0.95
- P08190 · AlphaFold monomer V2.0 prediction for protein fimg (P08190) · a predicted model of the same protein · chain G against A, TM-score 0.88
- P08189 · AlphaFold monomer V2.0 prediction for protein fimf (P08189) · a predicted model of the same protein · chain F against A, TM-score 0.81
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 A0A0F3W955
- Every structure of UniProt P08189
- Every structure of UniProt P08190
- Every structure of UniProt P08191
- Elsewhere: RCSB PDB 6E15 · PDBe 6E15 · UniProt P31697 · UniProt A0A0F3W955 · UniProt P08189 · UniProt P08190 · UniProt P08191
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