MolNFT v1 · #129224 · protein
Crystal structure of the beta-lactamase oxa-163
5ODZ: “Crystal structure of the beta-lactamase oxa-163”. X-ray diffraction, 2 ligands (MG, CL), 3 pockets (best druggability 0.77). MolNFT v1 #129224 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ODZ
- Type
- protein
- Length
- 477 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- F6KZJ2
- Ligands
- MG, CL
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Beta-lactamase (EC 3.5.2.6) | protein | 238 | 39% helix, 21% strand | F6KZJ2 |
| D | Beta-lactamase (EC 3.5.2.6) | protein | 239 | 41% helix, 20% strand | F6KZJ2 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains B, D
- CL · Chloride ion · ion · 4 copies · chains B, D
- PGE · Triethylene glycol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 653 | 0.77 | 0.82 | 96 | CL, MG |
| 2 | 53 | 0.39 | 0.81 | 17 | empty |
| 3 | 50 | 0.25 | 0.73 | 14 | CL |
Interfaces
1 interface between chains.
- B–D · 995 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 5ODZ · Crystal structure of the beta-lactamase oxa-163 · the same entry in another collection · chain B against B, 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 F6KZJ2
- Elsewhere: RCSB PDB 5ODZ · PDBe 5ODZ · UniProt F6KZJ2
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