MolNFT v1 · #155799 · protein
Crystal structure of ndm-1 in complex with D-captopril derivative WSS02120
6LIZ · Metallo-beta-lactamase type 2: “Crystal structure of ndm-1 in complex with D-captopril derivative WSS02120”. X-ray diffraction, 2 ligands (EEO, ZN), 1 pocket (best druggability 0.47). MolNFT v1 #155799 on GenesisL1: 3D structure…
- PDB
- 6LIZ
- Type
- protein
- Length
- 227 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
- EEO, ZN
- Pockets
- 1 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metallo-beta-lactamase type 2 (EC 3.5.2.6) | protein | 227 | 27% helix, 30% strand | C7C422 |
Ligands and binding sites
- EEO · (2R)-1-[(2S)-2-methyl-3-sulfanyl-propanoyl]azepane-2-carboxylic 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 | 186 | 0.47 | 0.75 | 24 | EEO |
Compared structures
- 6LIZ · Crystal structure of NDM-1 in complex with D-captopril derivative wss02120 · the same entry in another collection · chain A against A, TM-score 1.00
- C7C422 · AlphaFold monomer V2.0 prediction for metallo-beta-lactamase type 2 (C7C422) · a predicted model of the same protein · 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 C7C422
- Elsewhere: RCSB PDB 6LIZ · PDBe 6LIZ · UniProt C7C422
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