Research workbench
Crystal structure of ndm-1 in complex with triazole-based inhibitor OP31
Analyse Crystal structure of ndm-1 in complex with triazole-based inhibitor OP31 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TGD
- Type
- protein
- Length
- 460 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallo-beta-lactamase ndm-1
- UniProt
- M4JT39
- Ligands
- N8Q, ZN, CA
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metallo-beta-lactamase ndm-1 | protein | 229 | 27% helix, 30% strand | M4JT39 |
| B | Metallo-beta-lactamase ndm-1 | protein | 231 | 25% helix, 30% strand | M4JT39 |
Ligands and binding sites
- N8Q · 4-[[(2~{S})-oxolan-2-yl]methyl]-3-pyridin-3-yl-1~{H}-1, 2,4-triazole-5-thione · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 99 | 0.78 | 0.99 | 20 | empty |
| 2 | 112 | 0.56 | 0.85 | 30 | empty |
| 3 | 124 | 0.42 | 0.75 | 22 | ZN, N8Q |
| 4 | 121 | 0.36 | 0.73 | 25 | ZN, N8Q |
Interfaces
1 interface between chains.
- A–B · 939 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6TGD · Crystal structure of NDM-1 in complex with triazole-based inhibitor OP31 · 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 M4JT39
- Elsewhere: RCSB PDB 6TGD · PDBe 6TGD · UniProt M4JT39
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