MolNFT v1 · #168462 · protein
Class C beta-lactamase from escherichia COLI in complex with cephalothin
6WHF: “Class C beta-lactamase from escherichia COLI in complex with cephalothin”. X-ray diffraction, 1 ligand (9EP), 7 pockets (best druggability 0.75). MolNFT v1 #168462 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6WHF
- Type
- protein
- Length
- 718 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q104Z6
- Ligands
- 9EP
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase (EC 3.5.2.6) | protein | 359 | 40% helix, 23% strand | Q104Z6 |
Ligands and binding sites
- 9EP · (2R)-5-[(acetyloxy)methyl]-2-{(1R)-2-oxo-1-[(thiophen-2-ylacetyl)amino]ethyl}-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 9 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 | 783 | 0.75 | 0.79 | 89 | EDO, 9EP |
| 2 | 347 | 0.67 | 0.81 | 53 | EDO, 9EP |
| 3 | 88 | 0.38 | 0.77 | 17 | empty |
| 4 | 86 | 0.36 | 0.76 | 16 | empty |
| 5 | 81 | 0.32 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 357 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6WHF · class C beta-lactamase from Escherichia coli in complex with cephalothin · 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 Q104Z6
- Elsewhere: RCSB PDB 6WHF · PDBe 6WHF · UniProt Q104Z6
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