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Crystal structure of oxa-10 beta-lactamase covalently bound to cyclobutanone beta-lactam mimic
Analyse Crystal structure of oxa-10 beta-lactamase covalently bound to cyclobutanone… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LCE
- Type
- protein
- Length
- 982 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase oxa-10
- EC
- 3.5.2.6
- UniProt
- P14489
- Ligands
- LCE, PO4
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase oxa-10 (EC 3.5.2.6) | protein | 245 | 38% helix, 22% strand | P14489 |
| C, D | Beta-lactamase oxa-10 (EC 3.5.2.6) | protein | 246 | 41% helix, 23% strand | P14489 |
Ligands and binding sites
- LCE · (1S,3S,4S,5S)-7,7-dichloro-3-methoxy-2-thiabicyclo[3.2.0]heptan-6-one-4-carboxylic acid · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains C, A, D
- GOL · Glycerol · additive · 11 copies · chains A, C, B, 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 | 295 | 0.78 | 0.90 | 65 | GOL |
| 2 | 139 | 0.72 | 0.92 | 37 | GOL |
| 3 | 116 | 0.70 | 0.92 | 31 | GOL |
| 4 | 707 | 0.69 | 0.76 | 101 | GOL, LCE, PO4 |
| 5 | 174 | 0.45 | 0.75 | 28 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1405 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1349 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 577 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 modified (disulfide, carboxylation).
Compared structures
- 3LCE · Crystal Structure of Oxa-10 Beta-Lactamase Covalently Bound to Cyclobuta Beta-Lactam Mimic · the same entry in another collection · chain D against D, TM-score 1.00
- P14489 · AlphaFold monomer V2.0 prediction for beta-lactamase oxa-10 (P14489) · a predicted model of the same protein · chain B 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 P14489
- Elsewhere: RCSB PDB 3LCE · PDBe 3LCE · UniProt P14489
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