MolNFT v1 · #161077 · protein
Crystal structure of ndm-1 beta-lactamase in complex with broad spectrum boronic inhibitor CPD3
6Q2Y · Metallo-beta-lactamase type 2: “Crystal structure of ndm-1 beta-lactamase in complex with broad spectrum boronic inhibitor CPD3”. X-ray diffraction, 3 ligands (HCQ, ZN, CA), 4 pockets (best druggability 0.79). MolNFT v1 #161077 on…
- PDB
- 6Q2Y
- Type
- protein
- Length
- 460 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
- HCQ, ZN, CA
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metallo-beta-lactamase type 2 (EC 3.5.2.6) | protein | 231 | 25% helix, 30% strand | C7C422 |
| B | Metallo-beta-lactamase type 2 (EC 3.5.2.6) | protein | 229 | 25% helix, 30% strand | C7C422 |
Ligands and binding sites
- HCQ · [5-(aminomethyl)-1-benzothiophen-2-yl]-tris(oxidanyl) boranuide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- CA · Calcium ion · metal · 4 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
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 | 103 | 0.79 | 0.99 | 21 | empty |
| 2 | 81 | 0.47 | 0.83 | 25 | empty |
| 3 | 121 | 0.41 | 0.75 | 27 | HCQ |
| 4 | 81 | 0.33 | 0.74 | 21 | HCQ |
Interfaces
1 interface between chains.
- A–B · 941 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6Q2Y · Crystal structure of NDM-1 beta-lactamase in complex with broad spectrum boronic… · 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 0.99
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 6Q2Y · PDBe 6Q2Y · UniProt C7C422
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