MolNFT v1 · #155750 · protein
Crystal structure of gold-bound ndm-1
6LHE · Metallo-beta-lactamase type 2: “Crystal structure of gold-bound ndm-1”. X-ray diffraction, 2 ligands (AU, SO4), 4 pockets (best druggability 0.79). MolNFT v1 #155750 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6LHE
- Type
- protein
- Length
- 449 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
- AU, SO4
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metallo-beta-lactamase type 2 (EC 3.5.2.6) | protein | 226 | 24% helix, 31% strand | C7C422 |
| B | Metallo-beta-lactamase type 2 (EC 3.5.2.6) | protein | 223 | 26% helix, 30% strand | C7C422 |
Ligands and binding sites
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 | 110 | 0.79 | 0.98 | 20 | empty |
| 2 | 104 | 0.52 | 0.83 | 26 | empty |
| 3 | 82 | 0.30 | 0.73 | 19 | AU |
| 4 | 50 | 0.26 | 0.74 | 18 | AU |
Interfaces
1 interface between chains.
- A–B · 899 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
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 6LHE · PDBe 6LHE · UniProt C7C422
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