Research workbench
Oxa-10 class D beta-lactamase partially acylated with reacted 6BETA- (1-hydroxy-1-methylethyl) penicillanic acid
Analyse Oxa-10 class D beta-lactamase partially acylated with reacted 6BETA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1K54
- Type
- protein
- Length
- 973 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
- HOQ, SO4
- Pockets
- 14 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta lactamase oxa-10 (EC 3.5.2.6) | protein | 244 | 38% helix, 23% strand | P14489 |
| B | Beta lactamase oxa-10 (EC 3.5.2.6) | protein | 245 | 38% helix, 23% strand | P14489 |
| C | Beta lactamase oxa-10 (EC 3.5.2.6) | protein | 240 | 40% helix, 23% strand | P14489 |
| D | Beta lactamase oxa-10 (EC 3.5.2.6) | protein | 244 | 40% helix, 23% strand | P14489 |
Ligands and binding sites
- HOQ · (1R)-2-(1-carboxy-2-hydroxy-2-methyl-propyl)-5,5-dimethyl-thiazolidine-4-carboxylic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 17 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.70 | 0.90 | 32 | EDO |
| 2 | 127 | 0.70 | 0.91 | 29 | EDO |
| 3 | 112 | 0.69 | 0.91 | 31 | EDO |
| 4 | 119 | 0.65 | 0.88 | 27 | empty |
| 5 | 270 | 0.60 | 0.79 | 40 | SO4 |
Interfaces
3 interfaces between chains.
- A–C · 1427 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 1412 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 628 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 covalent, 2 modified (disulfide, covalent ligand, 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 1K54 · PDBe 1K54 · UniProt P14489
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