Research workbench
Cryo-EM structure of E. COLI P pilus tip assembly intermediate papc- papd-papk-papg in the second conformation
Analyse Cryo-EM structure of E. COLI P pilus tip assembly intermediate papc… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LHH
- Type
- protein
- Length
- 1,494 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- P fimbrial usher protein papc; Chaperone protein papd; Fimbrial adapter papk; P fimbria…
- UniProt
- A0A773A954, P15319, P62532, A0A798R8B8
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · 4 distinct chains · 3% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | P fimbrial usher protein papc | protein | 806 | 3% helix, 45% strand | A0A773A954 |
| D | Chaperone protein papd | protein | 215 | 2% helix, 41% strand | P15319 |
| K | Fimbrial adapter papk | protein | 157 | 3% helix, 34% strand | P62532 |
| G | P fimbria tip G-adhesin papg-II | protein | 316 | 1% helix, 34% strand | A0A798R8B8 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1025 | 0.90 | 0.91 | 130 | empty |
| 2 | 921 | 0.88 | 0.90 | 126 | empty |
| 3 | 609 | 0.86 | 0.91 | 86 | empty |
| 4 | 609 | 0.85 | 0.90 | 80 | empty |
| 5 | 1145 | 0.83 | 0.84 | 108 | empty |
Interfaces
5 interfaces between chains.
- C–G · 2090 Ų buried · 14 hydrogen bonds · protein-protein
- D–K · 1701 Ų buried · 27 hydrogen bonds · protein-protein
- K–G · 979 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 821 Ų buried · 3 hydrogen bonds · protein-protein
- D–G · 153 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7LHH · Cryo-EM structure of E. coli P pilus tip assembly intermediate PapC-PapD-PapK-PapG in the… · the same entry in another collection · chain C against C, TM-score 1.00
- P15319 · AlphaFold monomer V2.0 prediction for chaperone protein papd (P15319) · a predicted model of the same protein · chain D against A, TM-score 0.93
- P62532 · AlphaFold monomer V2.0 prediction for fimbrial adapter papk (P62532) · a predicted model of the same protein · chain K 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 A0A773A954
- Every structure of UniProt P15319
- Every structure of UniProt P62532
- Every structure of UniProt A0A798R8B8
- Elsewhere: RCSB PDB 7LHH · PDBe 7LHH · UniProt A0A773A954 · UniProt P15319 · UniProt P62532 · UniProt A0A798R8B8
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