MolNFT v1 · #141792 · protein
Crystal structure of ndm-1 in complex with D-captopril derivative CY32
5ZJ8 · Metallo-beta-lactamase type 2: “Crystal structure of ndm-1 in complex with D-captopril derivative CY32”. X-ray diffraction, 2 ligands (9DC, ZN), 2 pockets (best druggability 0.40). MolNFT v1 #141792 on GenesisL1: 3D structure…
- PDB
- 5ZJ8
- 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
- 9DC, ZN
- Pockets
- 2 · best druggability 0.40
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metallo-beta-lactamase type 2 (EC 3.5.2.6) | protein | 229 | 25% helix, 30% strand | C7C422 |
Ligands and binding sites
- 9DC · (2S)-2,3-disulfanylpropan-1-ol · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.40 | 0.76 | 19 | 9DC |
| 2 | 57 | 0.34 | 0.78 | 14 | EDO |
Compared structures
- 5ZJ8 · Crystal structure of NDM-1 in complex with D-captopril derivative CY32 · 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 5ZJ8 · PDBe 5ZJ8 · UniProt C7C422
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.