MolNFT v1 · #108642 · protein
Crystal structure of dim-1 metallo-beta-lactamase
4WD6: “Crystal structure of dim-1 metallo-beta-lactamase”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.72). MolNFT v1 #108642 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4WD6
- Type
- protein
- Length
- 433 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallo-beta-lactamase
- UniProt
- D5JGF6
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metallo-beta-lactamase | protein | 219 | 27% helix, 31% strand | D5JGF6 |
| B | Metallo-beta-lactamase | protein | 214 | 28% helix, 30% strand | D5JGF6 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1022 | 0.72 | 0.75 | 68 | ZN |
| 2 | 76 | 0.30 | 0.73 | 16 | ZN |
Interfaces
1 interface between chains.
- A–B · 314 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4WD6 · Crystal Structure of DIM-1 metallo-beta-lactamase · 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 D5JGF6
- Elsewhere: RCSB PDB 4WD6 · PDBe 4WD6 · UniProt D5JGF6
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