MolNFT v1 · #141709 · protein
Crystal structure of ndm-1 at PH7.5 (tris-hcl, (NH4)2SO4) in complex with hydrolyzed ampicillin
5ZGQ · Metallo-beta-lactamase type 2: “Crystal structure of ndm-1 at PH7.5 (tris-hcl, (NH4)2SO4) in complex with hydrolyzed ampicillin”. X-ray diffraction, 3 ligands (ZZ7, ZN, OH), 4 pockets (best druggability 0.77). MolNFT v1 #141709 on…
- PDB
- 5ZGQ
- Type
- protein
- Length
- 482 residues
- Chains
- 2
- 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
- ZZ7, ZN, OH
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Metallo-beta-lactamase type 2 (EC 3.5.2.6) | protein | 241 | 25% 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
- ZN · Zinc ion · metal · 4 copies · chains A, B
- OH · Hydroxide ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.77 | 0.98 | 20 | empty |
| 2 | 159 | 0.45 | 0.75 | 28 | OH, ZZ7 |
| 3 | 63 | 0.44 | 0.83 | 20 | empty |
| 4 | 140 | 0.43 | 0.76 | 24 | OH, ZZ7 |
Interfaces
1 interface between chains.
- A–B · 880 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5ZGQ · Crystal structure of NDM-1 at pH7.5 (Tris-HCl, (NH4)2SO4) in complex with hydrolyzed… · 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 5ZGQ · PDBe 5ZGQ · UniProt C7C422
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