Research workbench
Blac E166A cdc-1 acyl-intermediate
Analyse Blac E166A cdc-1 acyl-intermediate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VFH
- 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
- P0C5C1
- Ligands
- CD6, PO4
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-lactamase (EC 3.5.2.6) | protein | 265 | 42% helix, 17% strand | P0C5C1 |
Ligands and binding sites
- CD6 · (2R)-5-methylidene-2-{(1R)-2-oxo-1-[(phenylacetyl)amino]ethyl}-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid · ligand · 2 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 7 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 | 271 | 0.69 | 0.85 | 39 | PO4 |
| 2 | 154 | 0.69 | 0.89 | 30 | PO4 |
| 3 | 601 | 0.67 | 0.77 | 58 | CD6 |
| 4 | 488 | 0.62 | 0.76 | 43 | CD6 |
| 5 | 262 | 0.52 | 0.75 | 49 | empty |
Interfaces
4 interfaces between chains.
- A–B · 898 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 762 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 627 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 611 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3VFH · BlaC E166A CDC-1 Acyl-Intermediate · 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 P0C5C1
- Elsewhere: RCSB PDB 3VFH · PDBe 3VFH · UniProt P0C5C1
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