MolNFT v1 · #90325 · protein
Crystal structure of a hypothetical metallo-beta-lactamase from burkholderia pseudomallei
4EFZ · Metallo-beta-lactamase family protein: “Crystal structure of a hypothetical metallo-beta-lactamase from burkholderia pseudomallei”. X-ray diffraction, 3 ligands (CA, CL, SO4), 3 pockets (best druggability 0.62). MolNFT v1 #90325 on…
- PDB
- 4EFZ
- Type
- protein
- Length
- 584 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallo-beta-lactamase family protein
- UniProt
- Q3JRV4
- Ligands
- CA, CL, SO4
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metallo-beta-lactamase family protein | protein | 295 | 25% helix, 24% strand | Q3JRV4 |
| B | Metallo-beta-lactamase family protein | protein | 289 | 26% helix, 25% strand | Q3JRV4 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 586 | 0.62 | 0.74 | 58 | CL, GOL, SO4, EDO |
| 2 | 227 | 0.58 | 0.79 | 33 | EDO |
| 3 | 238 | 0.57 | 0.79 | 42 | CA |
Interfaces
1 interface between chains.
- A–B · 231 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4EFZ · Crystal Structure of a hypothetical metallo-beta-lactamase from Burkholderia pseudomallei · the same entry in another collection · chain A against A, TM-score 1.00
- Q3JRV4 · AlphaFold monomer V2.0 prediction for probable metallo-hydrolase BURPS1710B_2304 (Q3JRV4) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q3JRV4
- Elsewhere: RCSB PDB 4EFZ · PDBe 4EFZ · UniProt Q3JRV4
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