Research workbench
The cryo-electron microscopy structure of the type 1 chaperone-usher pilus rod
Analyse The cryo-electron microscopy structure of the type 1 chaperone-usher pilus rod in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OH0
- Type
- protein
- Length
- 942 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type-1 fimbrial protein, a chain
- UniProt
- P04128
- Pockets
- 16 · best druggability 0.77
Structure
electron microscopy · 1 distinct chain · 4% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Type-1 fimbrial protein, a chain | protein | 157 | 4% helix, 36% strand | P04128 |
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 791 | 0.77 | 0.81 | 74 | empty |
| 2 | 382 | 0.66 | 0.80 | 59 | empty |
| 3 | 266 | 0.63 | 0.81 | 41 | empty |
| 4 | 212 | 0.55 | 0.79 | 34 | empty |
| 5 | 239 | 0.55 | 0.78 | 38 | empty |
Interfaces
14 interfaces between chains.
- B–C · 1660 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 1652 Ų buried · 36 hydrogen bonds · protein-protein
- D–E · 1645 Ų buried · 35 hydrogen bonds · protein-protein
- E–F · 1642 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 1627 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5OH0 · The Cryo-Electron Microscopy Structure of the Type 1 Chaperone-Usher Pilus Rod · the same entry in another collection · chain F against F, TM-score 1.00
- P04128 · AlphaFold monomer V2.0 prediction for type-1 fimbrial protein, a chain (P04128) · a predicted model of the same protein · chain E against A, TM-score 0.93
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 P04128
- Elsewhere: RCSB PDB 5OH0 · PDBe 5OH0 · UniProt P04128
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