MolNFT v1 · #166568 · protein
Crystal structure of minor pseudopilin ternary complex of xcpvwx from the type 2 secretion system of pseudomonas aeruginosa in the P3 space group
6UTU · Type II secretion system protein I: “Crystal structure of minor pseudopilin ternary complex of xcpvwx from the type 2 secretion system of…”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.76). MolNFT v1 #166568 on…
- PDB
- 6UTU
- Type
- protein
- Length
- 1,421 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type II secretion system protein I; Type II secretion system protein J; Type II secretion…
- UniProt
- Q00516, Q00517, Q00518
- Ligands
- CA
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 9 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type II secretion system protein I | protein | 63 | 29% helix, 32% strand | Q00516 |
| B | Type II secretion system protein J | protein | 162 | 14% helix, 40% strand | Q00517 |
| C | Type II secretion system protein K | protein | 261 | 40% helix, 16% strand | Q00518 |
| D | Type II secretion system protein I | protein | 72 | 22% helix, 44% strand | Q00516 |
| E | Type II secretion system protein J | protein | 161 | 14% helix, 39% strand | Q00517 |
| F | Type II secretion system protein K | protein | 238 | 42% helix, 16% strand | Q00518 |
| G | Type II secretion system protein I | protein | 58 | 28% helix, 26% strand | Q00516 |
| H | Type II secretion system protein J | protein | 159 | 13% helix, 38% strand | Q00517 |
| I | Type II secretion system protein K | protein | 247 | 42% helix, 15% strand | Q00518 |
Ligands and binding sites
- CA · Calcium ion · metal · 9 copies · chains C, F, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1044 | 0.76 | 0.78 | 91 | empty |
| 2 | 166 | 0.71 | 0.90 | 18 | empty |
| 3 | 611 | 0.71 | 0.79 | 78 | empty |
| 4 | 360 | 0.71 | 0.83 | 42 | empty |
| 5 | 528 | 0.70 | 0.80 | 55 | empty |
Interfaces
12 interfaces between chains.
- B–C · 1512 Ų buried · 27 hydrogen bonds · protein-protein
- E–F · 1427 Ų buried · 29 hydrogen bonds · protein-protein
- H–I · 1426 Ų buried · 23 hydrogen bonds · protein-protein
- D–E · 645 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 608 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6UTU · Crystal structure of minor pseudopilin ternary complex of XcpVWX from the Type 2… · the same entry in another collection · chain I against I, 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 F against A, TM-score 0.99
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 Q00516
- Every structure of UniProt Q00517
- Every structure of UniProt Q00518
- Elsewhere: RCSB PDB 6UTU · PDBe 6UTU · UniProt Q00516 · UniProt Q00517 · UniProt Q00518
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