MolNFT v1 · #179535 · protein
Beta-lactamase mixed with sulbactam, 60MS
7K8K: “Beta-lactamase mixed with sulbactam, 60MS”. X-ray diffraction, 3 ligands (0RN, TSL, PO4), 11 pockets (best druggability 0.74). MolNFT v1 #179535 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7K8K
- Type
- protein
- Length
- 1,060 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- A0A655AHQ9
- Ligands
- 0RN, TSL, PO4
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-lactamase (EC 3.5.2.6) | protein | 265 | 43% helix, 17% strand | A0A655AHQ9 |
Ligands and binding sites
- 0RN · Sulbactam · ligand · 2 copies · chains A, B, C, D
- TSL · Trans-enamine intermediate of sulbactam · ligand · 2 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 872 | 0.74 | 0.79 | 81 | 0RN, PO4, TSL |
| 2 | 178 | 0.67 | 0.87 | 32 | 0RN, PO4 |
| 3 | 525 | 0.63 | 0.76 | 49 | TSL, PO4 |
| 4 | 104 | 0.47 | 0.80 | 23 | empty |
| 5 | 52 | 0.43 | 0.84 | 17 | empty |
Interfaces
4 interfaces between chains.
- A–B · 802 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 694 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 676 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 660 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7K8K · Beta-lactamase mixed with Sulbactam, 60ms · 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 A0A655AHQ9
- Elsewhere: RCSB PDB 7K8K · PDBe 7K8K · UniProt A0A655AHQ9
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