MolNFT v1 · #82512 · protein
Crystal structure of metallo-beta-lactamase smb-1
3VPE: “Crystal structure of metallo-beta-lactamase smb-1”. X-ray diffraction, 2 ligands (ZN, SO4), 1 pocket (best druggability 0.39). MolNFT v1 #82512 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3VPE
- Type
- protein
- Length
- 259 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallo-beta-lactamase
- EC
- 3.5.2.6
- UniProt
- G5ELM3
- Ligands
- ZN, SO4
- Pockets
- 1 · best druggability 0.39
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metallo-beta-lactamase (EC 3.5.2.6) | protein | 259 | 36% helix, 23% strand | G5ELM3 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
- GOL · Glycerol · additive · 4 copies · chains A
- ACT · Acetate ion · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.39 | 0.79 | 23 | ACT, GOL |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3VPE · Crystal Structure of Metallo-beta-Lactamase SMB-1 · 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 G5ELM3
- Elsewhere: RCSB PDB 3VPE · PDBe 3VPE · UniProt G5ELM3
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