Research workbench
Oxa-655_MEM. structural insights into the enhanced carbapenemase efficiency of oxa-655 compared to oxa-10.
Analyse Oxa-655_MEM. structural insights into the enhanced carbapenemase efficiency of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SKQ
- Type
- protein
- Length
- 980 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- A0A386YIZ1
- Ligands
- MER, SO4
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-lactamase (EC 3.5.2.6) | protein | 245 | 39% helix, 22% strand | A0A386YIZ1 |
Ligands and binding sites
- MER · (4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.71 | 0.94 | 28 | empty |
| 2 | 128 | 0.70 | 0.91 | 33 | empty |
| 3 | 98 | 0.67 | 0.91 | 24 | empty |
| 4 | 77 | 0.60 | 0.89 | 19 | empty |
| 5 | 142 | 0.42 | 0.75 | 25 | MER |
Interfaces
2 interfaces between chains.
- B–C · 1417 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1413 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 disulfide, 4 modified (covalent ligand, disulfide, carboxylation).
Compared structures
- 6SKQ · OXA-655_MEM. Structural insights into the enhanced carbapenemase efficiency of OXA-655… · 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 A0A386YIZ1
- Elsewhere: RCSB PDB 6SKQ · PDBe 6SKQ · UniProt A0A386YIZ1
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