Research workbench
Crystal structure of ndm-1 beta-lactamase in complex with boronic inhibitor cpd 5
Analyse Crystal structure of ndm-1 beta-lactamase in complex with boronic inhibitor cpd… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Q30
- Type
- protein
- Length
- 456 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
- HCH, ZN, CA
- Pockets
- 4 · 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 | 229 | 27% helix, 28% strand | C7C422 |
| B | Metallo-beta-lactamase type 2 (EC 3.5.2.6) | protein | 227 | 26% helix, 29% strand | C7C422 |
Ligands and binding sites
- HCH · (7-carboxy-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
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 | 104 | 0.79 | 0.98 | 21 | empty |
| 2 | 83 | 0.48 | 0.83 | 27 | empty |
| 3 | 77 | 0.34 | 0.75 | 19 | ZN, HCH |
| 4 | 50 | 0.32 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 949 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6Q30 · Crystal structure of NDM-1 beta-lactamase in complex with boronic inhibitor cpd 5 · 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 6Q30 · PDBe 6Q30 · UniProt C7C422
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.