Research workbench
Oxa-10_IPM. structural insight to the enhanced carbapenem efficiency of oxa-655 compared to oxa-10.
Analyse Oxa-10_IPM. structural insight to the enhanced carbapenem efficiency of oxa-655… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SKP
- Type
- protein
- Length
- 491 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q7BNC2
- Ligands
- IM2, NA
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 245 | 39% helix, 23% strand | Q7BNC2 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 246 | 37% helix, 24% strand | Q7BNC2 |
Ligands and binding sites
- IM2 · (5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A, B
- PGE · Triethylene glycol · additive · chains 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 136 | 0.70 | 0.91 | 31 | empty |
| 2 | 348 | 0.68 | 0.81 | 61 | IM2 |
| 3 | 106 | 0.37 | 0.75 | 20 | IM2 |
Interfaces
1 interface between chains.
- A–B · 1281 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 disulfide, 2 modified (covalent ligand, disulfide, carboxylation).
Compared structures
- 6SKP · OXA-10_IPM. Structural insight to the enhanced carbapenem efficiency of OXA-655 compared… · 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 Q7BNC2
- Elsewhere: RCSB PDB 6SKP · PDBe 6SKP · UniProt Q7BNC2
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