Research workbench
Crystal structure of ndm-1 metallo-beta-lactamase in complex with inhibitor X2
Analyse Crystal structure of ndm-1 metallo-beta-lactamase in complex with inhibitor X2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KZL
- Type
- protein
- Length
- 476 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- UniProt
- E5KIY2
- Ligands
- E1C, ZN, SO4
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase | protein | 244 | 24% helix, 29% strand | E5KIY2 |
| B | Beta-lactamase | protein | 232 | 24% helix, 31% strand | E5KIY2 |
Ligands and binding sites
- E1C · 2,5-diethyl-1-methyl-4-sulfamoyl-pyrrole-3-carboxylic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 6 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A
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 | 104 | 0.79 | 0.98 | 20 | empty |
| 2 | 172 | 0.51 | 0.78 | 28 | E1C |
| 3 | 85 | 0.40 | 0.78 | 22 | empty |
| 4 | 61 | 0.37 | 0.79 | 16 | empty |
| 5 | 98 | 0.36 | 0.74 | 18 | ZN, E1C |
Interfaces
1 interface between chains.
- A–B · 929 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6KZL · Crystal Structure Of NDM-1 Metallo-beta-lactamase In Complex With Inhibitor X2 · 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 6KZL · PDBe 6KZL · UniProt E5KIY2
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