Research workbench
Crystal structure of the class D beta-lactamases oxa-10 determined by mad phasing with selenomethionine
Analyse Crystal structure of the class D beta-lactamases oxa-10 determined by mad… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1K4E
- Type
- protein
- Length
- 491 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
- SO4
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase pse-2 (EC 3.5.2.6) | protein | 246 | 40% helix, 25% strand | P14489 |
| B | Beta-lactamase pse-2 (EC 3.5.2.6) | protein | 245 | 40% helix, 24% strand | P14489 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
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 | 122 | 0.69 | 0.90 | 32 | empty |
| 2 | 123 | 0.68 | 0.90 | 34 | empty |
| 3 | 86 | 0.40 | 0.78 | 20 | empty |
| 4 | 80 | 0.38 | 0.77 | 24 | empty |
| 5 | 87 | 0.34 | 0.74 | 16 | SO4 |
Interfaces
1 interface between chains.
- A–B · 1402 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified, 2 disulfide (engineered, disulfide, carboxylation).
Compared structures
- 1K4E · Crystal structure of the class D beta-lactamases oxa-10 determined by mad phasing with… · 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 1K4E · PDBe 1K4E · UniProt P14489
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.