MolNFT v1 · #141699 · protein
Crystal structure of ndm-1 at PH5.5 (bis-tris) in complex with hydrolyzed ampicillin
5ZGE · Metallo-beta-lactamase type 2: “Crystal structure of ndm-1 at PH5.5 (bis-tris) in complex with hydrolyzed ampicillin”. X-ray diffraction, 3 ligands (ZZ7, ZN, OH), 5 pockets (best druggability 0.78). MolNFT v1 #141699 on GenesisL1…
- PDB
- 5ZGE
- 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
- 5 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 24% 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 | 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
- 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
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 | 105 | 0.78 | 0.97 | 21 | empty |
| 2 | 94 | 0.57 | 0.86 | 34 | empty |
| 3 | 173 | 0.46 | 0.76 | 29 | ZZ7, OH |
| 4 | 143 | 0.42 | 0.75 | 27 | ZZ7, ZN, OH |
| 5 | 50 | 0.31 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 880 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5ZGE · Crystal structure of NDM-1 at pH5.5 (Bis-Tris) in complex with hydrolyzed 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 0.94
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 5ZGE · PDBe 5ZGE · UniProt C7C422
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.