Research workbench
Structure of acinetobacter baumannii carbapenemase oxa-239 K82D bound to imipenem
Analyse Structure of acinetobacter baumannii carbapenemase oxa-239 K82D bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WIB
- Type
- protein
- Length
- 481 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxa-239
- EC
- 3.5.2.1
- UniProt
- I6YCI1
- Ligands
- ID1
- Pockets
- 3 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxa-239 (EC 3.5.2.1) | protein | 243 | 38% helix, 23% strand | I6YCI1 |
| B | Oxa-239 (EC 3.5.2.1) | protein | 238 | 40% helix, 22% strand | I6YCI1 |
Ligands and binding sites
- ID1 · Imipenem · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 162 | 0.45 | 0.75 | 31 | empty |
| 2 | 176 | 0.45 | 0.74 | 27 | ID1 |
| 3 | 145 | 0.41 | 0.74 | 18 | ID1 |
Interfaces
1 interface between chains.
- A–B · 498 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5WIB · Structure of Acinetobacter baumannii carbapenemase OXA-239 K82D bound to imipenem · the same entry in another collection · chain A 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 I6YCI1
- Elsewhere: RCSB PDB 5WIB · PDBe 5WIB · UniProt I6YCI1
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