MolNFT v1 · #138414 · protein
Structure of new delhi metallo-beta-lactamase 4 (ndm-4)
5WIG: “Structure of new delhi metallo-beta-lactamase 4 (ndm-4)”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.44). MolNFT v1 #138414 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5WIG
- Type
- protein
- Length
- 458 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ndm-4
- UniProt
- A0A0G2ST15
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.44
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ndm-4 | protein | 229 | 27% helix, 31% strand | A0A0G2ST15 |
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
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 149 | 0.44 | 0.75 | 25 | ZN |
| 2 | 128 | 0.43 | 0.76 | 20 | ZN |
| 3 | 125 | 0.42 | 0.76 | 16 | empty |
| 4 | 74 | 0.30 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 198 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5WIG · Structure of New Delhi Metallo-Beta-lactamase 4 (NDM-4) · 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 A0A0G2ST15
- Elsewhere: RCSB PDB 5WIG · PDBe 5WIG · UniProt A0A0G2ST15
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