Research workbench
Oxa 10 class D beta-lactamase at pH 6.5
Analyse Oxa 10 class D beta-lactamase at pH 6.5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1K56
- Type
- protein
- Length
- 964 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- OXA10 beta-lactamase
- EC
- 3.5.2.6
- UniProt
- P14489
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | OXA10 beta-lactamase (EC 3.5.2.6) | protein | 243 | 39% helix, 23% strand | P14489 |
| B | OXA10 beta-lactamase (EC 3.5.2.6) | protein | 244 | 38% helix, 23% strand | P14489 |
| C | OXA10 beta-lactamase (EC 3.5.2.6) | protein | 236 | 39% helix, 23% strand | P14489 |
| D | OXA10 beta-lactamase (EC 3.5.2.6) | protein | 241 | 39% helix, 23% strand | P14489 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.71 | 0.92 | 30 | empty |
| 2 | 124 | 0.69 | 0.90 | 35 | empty |
| 3 | 121 | 0.68 | 0.90 | 31 | empty |
| 4 | 121 | 0.68 | 0.90 | 34 | empty |
| 5 | 342 | 0.58 | 0.76 | 49 | SO4 |
Interfaces
3 interfaces between chains.
- A–C · 1414 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1372 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 462 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 3 modified (disulfide, carboxylation).
Compared structures
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 P14489
- Elsewhere: RCSB PDB 1K56 · PDBe 1K56 · UniProt P14489
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