Research workbench
Crystal structure of the PapC usher bound to the chaperone-adhesin PapD-PapG
Analyse Crystal structure of the PapC usher bound to the chaperone-adhesin PapD-PapG in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CD2
- Type
- protein
- Length
- 1,258 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.7
- Source
- Escherichia coli
- Molecule
- Chaperone protein PapD; PapGII adhesin protein; Outer membrane usher protein PapC
- UniProt
- P15319, Q47450
- Pockets
- 17 · best druggability 0.87
Structure
x-ray diffraction · resolution 3.7 · 3 distinct chains · 3% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chaperone protein PapD | protein | 215 | 4% helix, 48% strand | P15319 |
| B | PapGII adhesin protein | protein | 316 | 2% helix, 51% strand | Q47450 |
| C | Outer membrane usher protein PapC | protein | 727 | 4% helix, 50% strand | — |
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1022 | 0.87 | 0.88 | 166 | empty |
| 2 | 1023 | 0.75 | 0.78 | 117 | empty |
| 3 | 596 | 0.73 | 0.81 | 70 | empty |
| 4 | 364 | 0.73 | 0.85 | 55 | empty |
| 5 | 443 | 0.70 | 0.80 | 54 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1867 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1118 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1051 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6CD2 · Crystal structure of the papc usher bound to the chaperone-adhesin papd-papg · the same entry in another collection · chain A against A, TM-score 1.00
- Q47450 · AlphaFold monomer V2.0 prediction for fimbrial adhesin papgii (Q47450) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P15319 · AlphaFold monomer V2.0 prediction for chaperone protein papd (P15319) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P15319
- Every structure of UniProt Q47450
- Elsewhere: RCSB PDB 6CD2 · PDBe 6CD2 · UniProt P15319 · UniProt Q47450
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