MolNFT v1 · #179534 · protein
Beta-lactamase mixed with ceftriaxone, 50MS
7K8H: “Beta-lactamase mixed with ceftriaxone, 50MS”. X-ray diffraction, 2 ligands (9F2, PO4), 10 pockets (best druggability 0.68). MolNFT v1 #179534 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7K8H
- 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
- 9F2, PO4
- Pockets
- 10 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-lactamase (EC 3.5.2.6) | protein | 265 | 46% helix, 17% strand | A0A655AHQ9 |
Ligands and binding sites
- 9F2 · Ceftriaxone · ligand · 4 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
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 | 444 | 0.68 | 0.80 | 65 | PO4 |
| 2 | 224 | 0.66 | 0.84 | 31 | PO4 |
| 3 | 333 | 0.56 | 0.75 | 36 | 9F2, PO4 |
| 4 | 356 | 0.55 | 0.74 | 34 | 9F2, PO4 |
| 5 | 148 | 0.44 | 0.76 | 34 | empty |
Interfaces
4 interfaces between chains.
- C–D · 708 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 702 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 672 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 628 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7K8H · Beta-lactamase mixed with Ceftriaxone, 50ms · 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 7K8H · PDBe 7K8H · UniProt A0A655AHQ9
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