MolNFT v1 · #162380 · protein
Structure of imp-13 metallo-beta-lactamase in apo form (loop closed)
6R78: “Structure of imp-13 metallo-beta-lactamase in apo form (loop closed)”. X-ray diffraction, 2 ligands (ZN, NA), 4 pockets (best druggability 0.69). MolNFT v1 #162380 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6R78
- Type
- protein
- Length
- 436 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- G8B4G1
- Ligands
- ZN, NA
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase (EC 3.5.2.6) | protein | 218 | 28% helix, 32% strand | G8B4G1 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · chains A
- GOL · Glycerol · additive · 9 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
- EDO · 1,2-ethanediol · additive · chains A
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 | 330 | 0.69 | 0.82 | 43 | empty |
| 2 | 157 | 0.50 | 0.78 | 24 | ZN, GOL |
| 3 | 164 | 0.50 | 0.78 | 22 | GOL |
| 4 | 84 | 0.36 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 775 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6R78 · Structure of IMP-13 metallo-beta-lactamase in apo form (loop closed) · 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 G8B4G1
- Elsewhere: RCSB PDB 6R78 · PDBe 6R78 · UniProt G8B4G1
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