MolNFT v1 · #105964 · protein
Structural and mechanistic insights into ndm-1 catalyzed hydrolysis of cephalosporins
4RL0 · Beta-lactamase ndm-1: “Structural and mechanistic insights into ndm-1 catalyzed hydrolysis of cephalosporins”. X-ray diffraction, 2 ligands (3S0, ZN), 2 pockets (best druggability 0.81). MolNFT v1 #105964 on GenesisL1: 3D structure…
- PDB
- 4RL0
- Type
- protein
- Length
- 469 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase ndm-1
- EC
- 3.5.2.6
- UniProt
- C7C422
- Ligands
- 3S0, ZN
- Pockets
- 2 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase ndm-1 (EC 3.5.2.6) | protein | 230 | 25% helix, 30% strand | C7C422 |
| B | Beta-lactamase ndm-1 (EC 3.5.2.6) | protein | 239 | 25% helix, 31% strand | C7C422 |
Ligands and binding sites
- 3S0 · (2R,5S)-5-[(carbamoyloxy)methyl]-2-[(R)-carboxy{[(2Z)-2-(furan-2-yl)-2-(methoxyimino)acetyl]amino}methyl]-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 959 | 0.81 | 0.83 | 92 | ZN, 3S0 |
| 2 | 50 | 0.32 | 0.77 | 9 | empty |
Interfaces
1 interface between chains.
- A–B · 770 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4RL0 · Structural and mechanistic insights into NDM-1 catalyzed hydrolysis of cephalosporins · the same entry in another collection · chain B against B, 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 0.98
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 4RL0 · PDBe 4RL0 · UniProt C7C422
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.