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Structure of the class D beta-lactamase oxa-10 in complex with a phenylboronic acid
Analyse Structure of the class D beta-lactamase oxa-10 in complex with a phenylboronic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1K6S
- Type
- protein
- Length
- 489 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase pse-2
- EC
- 3.5.2.6
- UniProt
- P14489
- Ligands
- IAP, CA, SO4
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase pse-2 (EC 3.5.2.6) | protein | 244 | 40% helix, 24% strand | P14489 |
| B | Beta-lactamase pse-2 (EC 3.5.2.6) | protein | 245 | 39% helix, 24% strand | P14489 |
Ligands and binding sites
- IAP · 4-iodo-acetamido phenylboronic acid · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 3 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
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 | 126 | 0.72 | 0.92 | 28 | empty |
| 2 | 144 | 0.71 | 0.91 | 34 | empty |
| 3 | 216 | 0.47 | 0.74 | 29 | IAP |
| 4 | 165 | 0.44 | 0.74 | 26 | CA, IAP |
| 5 | 52 | 0.37 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1305 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 2 disulfide, 2 modified (covalent ligand, disulfide, carboxylation).
Compared structures
- 1K6S · Structure of the class D beta-lactamase oxa-10 in complex with a phenylboronic acid · the same entry in another collection · chain A against A, TM-score 1.00
- P14489 · AlphaFold monomer V2.0 prediction for beta-lactamase oxa-10 (P14489) · a predicted model of the same protein · chain A 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 P14489
- Elsewhere: RCSB PDB 1K6S · PDBe 1K6S · UniProt P14489
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