MolNFT v1 · #159636 · protein
Crystal structure of the new delhi metallo-beta-lactamase-1 adduct with a lysine-targeted affinity label
6OVZ: “Crystal structure of the new delhi metallo-beta-lactamase-1 adduct with a lysine-targeted affinity label”. X-ray diffraction, 4 ligands (N9M, N9J, ZN), 1 pocket (best druggability 0.76). MolNFT v1 #159636 on GenesisL1: 3D structure…
- PDB
- 6OVZ
- Type
- protein
- Length
- 454 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- UniProt
- E5KIY2
- Ligands
- N9M, N9J, ZN, CA
- Pockets
- 1 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase | protein | 227 | 25% helix, 31% strand | E5KIY2 |
Ligands and binding sites
- N9M · benzyl (carboxyoxy)carbamate · ligand · chains A, B
- N9J · benzyl hydroxycarbamate · ligand · chains A, B
- ZN · Zinc ion · metal · 6 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- FMT · Formic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1075 | 0.76 | 0.79 | 88 | N9M, N9J, FMT |
Interfaces
1 interface between chains.
- A–B · 407 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct, covalent ligand).
Compared structures
- 6OVZ · Crystal structure of the New Delhi metallo-beta-lactamase-1 adduct with a lysine-targeted… · 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 E5KIY2
- Elsewhere: RCSB PDB 6OVZ · PDBe 6OVZ · UniProt E5KIY2
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