MolNFT v1 · #179531 · protein
Beta-lactamase mixed with ceftriaxone, 5MS
7K8E: “Beta-lactamase mixed with ceftriaxone, 5MS”. X-ray diffraction, 2 ligands (9F2, PO4), 9 pockets (best druggability 0.68). MolNFT v1 #179531 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7K8E
- 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
- 9 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-lactamase (EC 3.5.2.6) | protein | 265 | 45% helix, 16% strand | A0A655AHQ9 |
Ligands and binding sites
- 9F2 · Ceftriaxone · 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
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 273 | 0.68 | 0.84 | 37 | PO4 |
| 2 | 737 | 0.67 | 0.75 | 81 | 9F2, PO4 |
| 3 | 208 | 0.65 | 0.84 | 32 | PO4 |
| 4 | 440 | 0.60 | 0.76 | 36 | 9F2, PO4 |
| 5 | 273 | 0.54 | 0.76 | 47 | empty |
Interfaces
4 interfaces between chains.
- A–B · 769 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 745 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 621 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 588 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7K8E · Beta-lactamase mixed with Ceftriaxone, 5ms · 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 7K8E · PDBe 7K8E · UniProt A0A655AHQ9
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