MolNFT v1 · #152935 · protein
Dmpr-phenol complex of pseudomonas putida
6IY8 · Positive regulator capr: “Dmpr-phenol complex of pseudomonas putida”. X-ray diffraction, 2 ligands (IPH, ZN), 20 pockets (best druggability 0.81). MolNFT v1 #152935 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6IY8
- Type
- protein
- Length
- 1,871 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Positive regulator capr
- UniProt
- Q7WSM9
- Ligands
- IPH, ZN
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Positive regulator capr | protein | 469 | 45% helix, 17% strand | Q7WSM9 |
| B | Positive regulator capr | protein | 465 | 48% helix, 16% strand | Q7WSM9 |
| C | Positive regulator capr | protein | 468 | 46% helix, 17% strand | Q7WSM9 |
Ligands and binding sites
- IPH · Phenol · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 679 | 0.81 | 0.85 | 80 | empty |
| 2 | 801 | 0.80 | 0.84 | 87 | empty |
| 3 | 113 | 0.78 | 0.97 | 22 | empty |
| 4 | 925 | 0.77 | 0.80 | 100 | empty |
| 5 | 93 | 0.77 | 0.97 | 18 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3334 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 3268 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 2731 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1987 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1745 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6IY8 · DmpR-phenol complex of Pseudomonas putida · the same entry in another collection · chain A against A, TM-score 1.00
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 Q7WSM9
- Elsewhere: RCSB PDB 6IY8 · PDBe 6IY8 · UniProt Q7WSM9
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