Research workbench
Crystal structure of new delhi metallo-beta-lactamase-1, complexed with CD and ampicillin
Analyse Crystal structure of new delhi metallo-beta-lactamase-1, complexed with CD and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HL1
- Type
- protein
- Length
- 478 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, CL
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase ndm-1 (EC 3.5.2.6) | protein | 238 | 25% helix, 29% strand | C7C422 |
| B | Beta-lactamase ndm-1 (EC 3.5.2.6) | protein | 240 | 24% helix, 30% 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 · 6 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 103 | 0.78 | 0.98 | 21 | empty |
| 2 | 98 | 0.50 | 0.83 | 27 | empty |
| 3 | 221 | 0.50 | 0.76 | 33 | ZZ7, CL |
| 4 | 208 | 0.49 | 0.75 | 28 | ZZ7, CD, CL |
| 5 | 52 | 0.31 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 879 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4HL1 · Crystal Structure of New Delhi Metallo-beta-Lactamase-1, Complexed with Cd and Ampicillin · 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 0.95
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 4HL1 · PDBe 4HL1 · UniProt C7C422
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