MolNFT v1 · #137599 · protein
The crystal structure of minor pseudopilin ternary complex of xcpvwx from the type 2 secretion system of pseudomonas aeruginosa
5VTM · Type II secretion system protein J: “The crystal structure of minor pseudopilin ternary complex of xcpvwx from the type 2 secretion system of…”. X-ray diffraction, 1 ligand (CA), 8 pockets (best druggability 0.73). MolNFT v1 #137599…
- PDB
- 5VTM
- Type
- protein
- Length
- 505 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type II secretion system protein J; Type II secretion system protein K; Type II secretion…
- UniProt
- Q00517, Q00518, Q00516
- Ligands
- CA
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| W | Type II secretion system protein J | protein | 161 | 15% helix, 40% strand | Q00517 |
| X | Type II secretion system protein K | protein | 259 | 42% helix, 19% strand | Q00518 |
| V | Type II secretion system protein I | protein | 85 | 25% helix, 39% strand | Q00516 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 606 | 0.73 | 0.81 | 81 | empty |
| 2 | 298 | 0.59 | 0.78 | 34 | empty |
| 3 | 275 | 0.53 | 0.75 | 30 | empty |
| 4 | 64 | 0.53 | 0.87 | 18 | empty |
| 5 | 56 | 0.43 | 0.82 | 21 | empty |
Interfaces
3 interfaces between chains.
- W–X · 1720 Ų buried · 35 hydrogen bonds · protein-protein
- W–V · 754 Ų buried · 9 hydrogen bonds · protein-protein
- X–V · 624 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (engineered).
Compared structures
- 5VTM · The crystal structure of minor pseudopilin ternary complex of XcpVWX from the Type 2… · the same entry in another collection · chain W against W, TM-score 1.00
- Q00518 · AlphaFold monomer V2.0 prediction for type II secretion system protein K (Q00518) · a predicted model of the same protein · chain X against A, TM-score 0.99
- Q00517 · AlphaFold monomer V2.0 prediction for type II secretion system protein J (Q00517) · a predicted model of the same protein · chain W against A, TM-score 0.96
- Q00516 · AlphaFold monomer V2.0 prediction for type II secretion system protein I (Q00516) · a predicted model of the same protein · chain V against A, TM-score 0.96
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 Q00517
- Every structure of UniProt Q00518
- Every structure of UniProt Q00516
- Elsewhere: RCSB PDB 5VTM · PDBe 5VTM · UniProt Q00517 · UniProt Q00518 · UniProt Q00516
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