Research workbench
Oxa-48-like beta-lactamase oxa-436
Analyse Oxa-48-like beta-lactamase oxa-436 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ODA
- Type
- protein
- Length
- 964 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- A0A0S2C593
- Ligands
- CL
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-lactamase (EC 3.5.2.6) | protein | 241 | 41% helix, 21% strand | A0A0S2C593 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1014 | 0.79 | 0.81 | 123 | CL |
| 2 | 1123 | 0.78 | 0.80 | 140 | EDO, CL |
| 3 | 74 | 0.41 | 0.79 | 16 | empty |
| 4 | 117 | 0.39 | 0.75 | 23 | empty |
| 5 | 60 | 0.38 | 0.79 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1047 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1036 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 202 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 7ODA · OXA-48-like Beta-lactamase OXA-436 · 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 A0A0S2C593
- Elsewhere: RCSB PDB 7ODA · PDBe 7ODA · UniProt A0A0S2C593
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