MolNFT v1 · #128005 · protein
Crystal structure of metallo-beta-lactamase spm-1 in space group P4222
5NDE · Beta-lactamase imp-1: “Crystal structure of metallo-beta-lactamase spm-1 in space group P4222”. X-ray diffraction, 3 ligands (ZN, SO4, CL), 2 pockets (best druggability 0.79). MolNFT v1 #128005 on GenesisL1: 3D structure, binding…
- PDB
- 5NDE
- Type
- protein
- Length
- 491 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase imp-1
- EC
- 3.5.2.6
- UniProt
- Q8G9Q0
- Ligands
- ZN, SO4, CL
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase imp-1 (EC 3.5.2.6) | protein | 244 | 31% helix, 27% strand | Q8G9Q0 |
| B | Beta-lactamase imp-1 (EC 3.5.2.6) | protein | 247 | 32% helix, 27% strand | Q8G9Q0 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 499 | 0.79 | 0.86 | 59 | GOL, ZN |
| 2 | 456 | 0.76 | 0.85 | 46 | GOL |
Interfaces
1 interface between chains.
- A–B · 966 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5NDE · Crystal structure of metallo-beta-lactamase SPM-1 in space group P4222 · 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 Q8G9Q0
- Elsewhere: RCSB PDB 5NDE · PDBe 5NDE · UniProt Q8G9Q0
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