Research workbench
Crystal structure of oxa-48 with hydrolyzed imipenem
Analyse Crystal structure of oxa-48 with hydrolyzed imipenem in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PK0
- Type
- protein
- Length
- 975 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxa family beta-lactamase
- UniProt
- A0A482LRD5
- Ligands
- HIW, CL
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxa family beta-lactamase | protein | 244 | 41% helix, 21% strand | A0A482LRD5 |
| B, C | Oxa family beta-lactamase | protein | 243 | 40% helix, 21% strand | A0A482LRD5 |
| D | Oxa family beta-lactamase | protein | 245 | 41% helix, 21% strand | A0A482LRD5 |
Ligands and binding sites
- HIW · (2R,4S)-2-[(1S,2R)-1-carboxy-2-hydroxypropyl]-4-[(2-{[(Z)-iminomethyl]amino}ethyl)sulfanyl]-3,4-dihydro-2H-pyrrole-5-carboxylic acid · ligand · 5 copies · chains A, C, B, D
- CL · Chloride ion · ion · 2 copies · chains A, B, C, D
- GOL · Glycerol · additive · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 735 | 0.78 | 0.82 | 110 | CL, HIW, GOL |
| 2 | 890 | 0.77 | 0.80 | 128 | HIW, CL |
| 3 | 268 | 0.55 | 0.77 | 27 | HIW |
| 4 | 134 | 0.43 | 0.76 | 21 | HIW |
| 5 | 75 | 0.38 | 0.78 | 15 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1007 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 963 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 298 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 6PK0 · Crystal Structure of OXA-48 with Hydrolyzed 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 6PK0 · PDBe 6PK0 · UniProt A0A482LRD5
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