MolNFT v1 · #153933 · protein
Crystal structure of metallo-beta-lactamase vmb-1
6JV4: “Crystal structure of metallo-beta-lactamase vmb-1”. X-ray diffraction, 1 ligand (ZN), 6 pockets (best druggability 0.83). MolNFT v1 #153933 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6JV4
- Type
- protein
- Length
- 882 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vmb-1
- UniProt
- A0A5Q5ADH9
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Vmb-1 | protein | 221 | 26% helix, 32% strand | A0A5Q5ADH9 |
| B, C | Vmb-1 | protein | 220 | 26% helix, 32% strand | A0A5Q5ADH9 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- CIT · Citric acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 962 | 0.83 | 0.85 | 118 | ZN, CIT |
| 2 | 309 | 0.57 | 0.76 | 38 | empty |
| 3 | 156 | 0.50 | 0.78 | 31 | ZN, CIT |
| 4 | 144 | 0.46 | 0.77 | 29 | empty |
| 5 | 74 | 0.31 | 0.74 | 18 | ZN, CIT |
Interfaces
4 interfaces between chains.
- A–C · 817 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 578 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 419 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 395 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6JV4 · Crystal structure of metallo-beta-lactamase VMB-1 · 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 A0A5Q5ADH9
- Elsewhere: RCSB PDB 6JV4 · PDBe 6JV4 · UniProt A0A5Q5ADH9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.