Research workbench
Crystal structure of ndm-1 at PH7.0 (hepes) with 2 molecules per asymmetric unit
Analyse Crystal structure of ndm-1 at PH7.0 (hepes) with 2 molecules per asymmetric unit in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZGU
- Type
- protein
- Length
- 481 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
- ZN, OH
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metallo-beta-lactamase type 2 (EC 3.5.2.6) | protein | 239 | 26% helix, 28% strand | C7C422 |
| B | Metallo-beta-lactamase type 2 (EC 3.5.2.6) | protein | 242 | 26% helix, 29% strand | C7C422 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- OH · Hydroxide ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains 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 | 1161 | 0.79 | 0.81 | 93 | ZN, OH, EPE |
| 2 | 53 | 0.31 | 0.76 | 15 | empty |
| 3 | 54 | 0.26 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 912 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5ZGU · Crystal structure of NDM-1 at pH7.0 (HEPES) with 2 molecules per asymmetric unit · 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 0.99
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 5ZGU · PDBe 5ZGU · UniProt C7C422
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