MolNFT v1 · #145895 · protein
Crystal structure of ndm-1 complexed with compound 6
6D1D · Metallo-beta-lactamase type 2: “Crystal structure of ndm-1 complexed with compound 6”. X-ray diffraction, 2 ligands (GTV, ZN), 1 pocket (best druggability 0.39). MolNFT v1 #145895 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6D1D
- Type
- protein
- Length
- 229 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallo-beta-lactamase type 2
- EC
- 3.5.2.6
- UniProt
- C7C422
- Ligands
- GTV, ZN
- Pockets
- 1 · best druggability 0.39
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metallo-beta-lactamase type 2 (EC 3.5.2.6) | protein | 229 | 25% helix, 31% strand | C7C422 |
Ligands and binding sites
- GTV · [(5,7-dimethyl-2-oxo-2H-1-benzopyran-4-yl) methyl]phosphonic acid · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- ACT · Acetate ion · additive · 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 | 89 | 0.39 | 0.77 | 23 | ZN, GTV, ACT |
Compared structures
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 C7C422
- Elsewhere: RCSB PDB 6D1D · PDBe 6D1D · UniProt C7C422
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