Research workbench
Crystal structure of ndm-1 metallo-beta-lactamase in complex with inhibitor NO9
Analyse Crystal structure of ndm-1 metallo-beta-lactamase in complex with inhibitor NO9 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KXI
- Type
- protein
- Length
- 467 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- UniProt
- E5KIY2
- Ligands
- NO9, ZN, SO4
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase | protein | 236 | 23% helix, 31% strand | E5KIY2 |
| B | Beta-lactamase | protein | 231 | 24% helix, 31% strand | E5KIY2 |
Ligands and binding sites
- NO9 · 2,5-dimethyl-4-sulfamoyl-furan-3-carboxylic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 6 copies · chains A, B
- SO4 · Sulfate ion · ion · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 109 | 0.79 | 0.98 | 20 | empty |
| 2 | 84 | 0.52 | 0.85 | 29 | empty |
| 3 | 145 | 0.52 | 0.80 | 25 | NO9 |
| 4 | 122 | 0.39 | 0.75 | 21 | SO4, NO9 |
Interfaces
1 interface between chains.
- A–B · 950 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6KXI · Crystal Structure Of NDM-1 Metallo-beta-lactamase In Complex With Inhibitor NO9 · the same entry in another collection · chain A against A, TM-score 1.00
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 E5KIY2
- Elsewhere: RCSB PDB 6KXI · PDBe 6KXI · UniProt E5KIY2
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