Research workbench
Crystal structure of ndm-1 bound to hydrolyzed benzylpenicillin
Analyse Crystal structure of ndm-1 bound to hydrolyzed benzylpenicillin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EYF
- 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
- PNK, ZN
- Pockets
- 3 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase ndm-1 (EC 3.5.2.6) | protein | 241 | 24% helix, 31% strand | C7C422 |
Ligands and binding sites
- PNK · (2R,4S)-2-{(R)-carboxy[(phenylacetyl)amino]methyl}-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 666 | 0.83 | 0.88 | 68 | PNK, ZN |
| 2 | 147 | 0.49 | 0.78 | 31 | empty |
| 3 | 111 | 0.44 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 855 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4EYF · Crystal structure of NDM-1 bound to hydrolyzed benzylpenicillin · 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 B 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 4EYF · PDBe 4EYF · UniProt C7C422
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