Research workbench
Structure of the P pilus usher (papc) translocation pore
Analyse Structure of the P pilus usher (papc) translocation pore in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VQI
- Type
- protein
- Length
- 954 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer membrane usher protein papc
- UniProt
- P07110
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 67% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Outer membrane usher protein papc | protein | 477 | 3% helix, 67% strand | P07110 |
| B | Outer membrane usher protein papc | protein | 477 | 3% helix, 67% strand | P07110 |
Ligands and binding sites
- LDA · Lauryl dimethylamine-N-oxide · additive · 2 copies · chains A, B
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1172 | 0.79 | 0.81 | 121 | empty |
| 2 | 881 | 0.79 | 0.82 | 106 | empty |
| 3 | 1000 | 0.78 | 0.80 | 125 | empty |
| 4 | 894 | 0.71 | 0.76 | 108 | empty |
| 5 | 325 | 0.64 | 0.81 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 1248 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 2VQI · Structure of the P pilus usher (PapC) translocation pore · the same entry in another collection · chain B against B, TM-score 1.00
- P07110 · AlphaFold monomer V2.0 prediction for outer membrane usher protein papc (P07110) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P07110
- Elsewhere: RCSB PDB 2VQI · PDBe 2VQI · UniProt P07110
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