MolNFT v1 · #169666 · protein
Biuret hydrolase (biuh) from rhodococcus sp. mel C169S bound with biuret
6XJM: “Biuret hydrolase (biuh) from rhodococcus sp. mel C169S bound with biuret”. X-ray diffraction, 1 ligand (C5J), 5 pockets (best druggability 0.87). MolNFT v1 #169666 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6XJM
- Type
- protein
- Length
- 911 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Biuret hydrolase
- UniProt
- H8ZKV9
- Ligands
- C5J
- Pockets
- 5 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Biuret hydrolase | protein | 226 | 40% helix, 22% strand | H8ZKV9 |
| B | Biuret hydrolase | protein | 227 | 38% helix, 19% strand | H8ZKV9 |
| C | Biuret hydrolase | protein | 228 | 38% helix, 22% strand | H8ZKV9 |
| D | Biuret hydrolase | protein | 230 | 39% helix, 20% strand | H8ZKV9 |
Ligands and binding sites
- C5J · dicarbonimidic diamide · ligand · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 513 | 0.87 | 0.94 | 44 | empty |
| 2 | 286 | 0.61 | 0.80 | 33 | empty |
| 3 | 282 | 0.61 | 0.79 | 34 | empty |
| 4 | 282 | 0.60 | 0.79 | 33 | empty |
| 5 | 316 | 0.59 | 0.77 | 36 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2019 Ų buried · 40 hydrogen bonds · protein-protein
- A–D · 2009 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 858 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 846 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 234 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6XJM · Biuret Hydrolase (BiuH) from Rhodococcus sp. Mel C169S bound with biuret · 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 H8ZKV9
- Elsewhere: RCSB PDB 6XJM · PDBe 6XJM · UniProt H8ZKV9
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