MolNFT v1 · #105645 · protein
Crystal structure of new delhi metallo-beta-lactamase-1 mutant M67V complexed with hydrolyzed ampicillin
4RAW · Beta-lactamase ndm-1: “Crystal structure of new delhi metallo-beta-lactamase-1 mutant M67V complexed with hydrolyzed ampicillin”. X-ray diffraction, 2 ligands (ZZ7, CD), 5 pockets (best druggability 0.77). MolNFT v1 #105645 on…
- PDB
- 4RAW
- Type
- protein
- Length
- 482 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
- ZZ7, CD
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase ndm-1 (EC 3.5.2.6) | protein | 241 | 24% helix, 29% strand | C7C422 |
Ligands and binding sites
- ZZ7 · (2R,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid · ligand · 2 copies · chains A, B
- CD · Cadmium ion · metal · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.77 | 0.98 | 21 | empty |
| 2 | 99 | 0.57 | 0.86 | 31 | empty |
| 3 | 148 | 0.45 | 0.76 | 31 | ZZ7 |
| 4 | 137 | 0.42 | 0.75 | 25 | ZZ7, CD |
| 5 | 50 | 0.30 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 885 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4RAW · Crystal Structure of New Delhi Metallo-beta-Lactamase-1 Mutant M67V Complexed with… · 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 0.94
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 4RAW · PDBe 4RAW · UniProt C7C422
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