MolNFT v1 · #158759 · protein
Crystal structure of ndm-1 D199N with compound 7
6O3R · Carbapenem hydrolyzing class B metallo beta lactamase ndm- 1: “Crystal structure of ndm-1 D199N with compound 7”. X-ray diffraction, 2 ligands (XJE, ZN), 1 pocket (best druggability 0.41). MolNFT v1 #158759 on GenesisL1: 3D…
- PDB
- 6O3R
- Type
- protein
- Length
- 229 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbapenem hydrolyzing class B metallo beta lactamase ndm- 1
- UniProt
- E9NWK5
- Ligands
- XJE, ZN
- Pockets
- 1 · best druggability 0.41
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carbapenem hydrolyzing class B metallo beta lactamase ndm- 1 | protein | 229 | 26% helix, 31% strand | E9NWK5 |
Ligands and binding sites
- XJE · [(5-methoxy-7-methyl-2-oxo-2H-1-benzopyran-4-yl) methyl]phosphonic acid · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 144 | 0.41 | 0.74 | 23 | ZN, XJE |
Compared structures
- 6O3R · Crystal Structure of NDM-1 D199N with Compound 7 · 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 E9NWK5
- Elsewhere: RCSB PDB 6O3R · PDBe 6O3R · UniProt E9NWK5
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