Research workbench
Crystal structure of class D beta-lactamase oxa-48 with imipenem
Analyse Crystal structure of class D beta-lactamase oxa-48 with imipenem in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PTU
- Type
- protein
- Length
- 975 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Class D carbapenemase oxa-48
- EC
- 3.5.2.6
- UniProt
- A0A482LRD5
- Ligands
- ID1, CL
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Class D carbapenemase oxa-48 (EC 3.5.2.6) | protein | 243 | 41% helix, 20% strand | A0A482LRD5 |
| B, C, D | Class D carbapenemase oxa-48 (EC 3.5.2.6) | protein | 244 | 40% helix, 21% strand | A0A482LRD5 |
Ligands and binding sites
- ID1 · Imipenem · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 919 | 0.79 | 0.81 | 128 | CL, ID1 |
| 2 | 911 | 0.78 | 0.81 | 125 | CL, ID1 |
| 3 | 179 | 0.48 | 0.76 | 19 | empty |
| 4 | 84 | 0.43 | 0.80 | 13 | empty |
| 5 | 63 | 0.37 | 0.79 | 17 | empty |
Interfaces
3 interfaces between chains.
- C–D · 986 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 971 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 301 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6PTU · Crystal Structure of Class D Beta-lactamase OXA-48 with 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 A0A482LRD5
- Elsewhere: RCSB PDB 6PTU · PDBe 6PTU · UniProt A0A482LRD5
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