Research workbench
Crystal structure of class D beta-lactamase oxa-48 with cefotaxime
Analyse Crystal structure of class D beta-lactamase oxa-48 with cefotaxime in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PQI
- Type
- protein
- Length
- 984 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Class D carbapenemase oxa-48
- EC
- 3.5.2.6
- UniProt
- A0A482LRD5
- Ligands
- CEF, CL
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Class D carbapenemase oxa-48 (EC 3.5.2.6) | protein | 247 | 40% helix, 20% strand | A0A482LRD5 |
| B | Class D carbapenemase oxa-48 (EC 3.5.2.6) | protein | 245 | 40% helix, 21% strand | A0A482LRD5 |
| C | Class D carbapenemase oxa-48 (EC 3.5.2.6) | protein | 248 | 40% helix, 22% strand | A0A482LRD5 |
| D | Class D carbapenemase oxa-48 (EC 3.5.2.6) | protein | 244 | 40% helix, 20% strand | A0A482LRD5 |
Ligands and binding sites
- CEF · CEFOTAXIME, C3' cleaved, open, bound form · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 3 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1021 | 0.81 | 0.83 | 129 | CEF, ACT |
| 2 | 509 | 0.79 | 0.86 | 84 | CL |
| 3 | 259 | 0.61 | 0.80 | 25 | empty |
| 4 | 157 | 0.52 | 0.79 | 22 | empty |
| 5 | 112 | 0.38 | 0.75 | 19 | CEF |
Interfaces
4 interfaces between chains.
- A–B · 982 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 738 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 711 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 231 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6PQI · Crystal Structure of Class D Beta-lactamase OXA-48 with Cefotaxime · 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 A0A482LRD5
- Elsewhere: RCSB PDB 6PQI · PDBe 6PQI · UniProt A0A482LRD5
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