MolNFT v1 · #164021 · protein
Oxa-10_ETP. structural insight to the enhanced carbapenem efficiency of oxa-655 compared to oxa-10.
6SKR · Beta-lactamase: “Oxa-10_ETP. structural insight to the enhanced carbapenem efficiency of oxa-655 compared to oxa-10.”. X-ray diffraction, 2 ligands (1RG, MG), 7 pockets (best druggability 0.73). MolNFT v1 #164021 on GenesisL1: 3D…
- PDB
- 6SKR
- Type
- protein
- Length
- 490 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
- 1RG, MG
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase (EC 3.5.2.6) | protein | 245 | 42% helix, 24% strand | Q7BNC2 |
Ligands and binding sites
- 1RG · (4R,5S)-3-({(3S,5S)-5-[(3-carboxyphenyl) carbamoyl]pyrrolidin-3-yl}sulfanyl)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A
- FMT · Formic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.73 | 0.92 | 31 | empty |
| 2 | 116 | 0.71 | 0.93 | 30 | empty |
| 3 | 193 | 0.49 | 0.76 | 34 | empty |
| 4 | 63 | 0.38 | 0.79 | 15 | empty |
| 5 | 94 | 0.37 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1411 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 disulfide, 2 modified (covalent ligand, disulfide, carboxylation).
Compared structures
- 6SKR · OXA-10_ETP. 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 6SKR · PDBe 6SKR · UniProt Q7BNC2
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