Research workbench
Cystathionine beta-lyase (cbl) from escherichia COLI in complex with N-hydrazinocarbonylmethyl-2-trifluoromethyl-benzamide
Analyse Cystathionine beta-lyase (cbl) from escherichia COLI in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FQ6
- Type
- protein
- Length
- 783 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cystathionine beta-lyase
- EC
- 4.4.1.8
- UniProt
- P06721
- Ligands
- P3F
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cystathionine beta-lyase (EC 4.4.1.8) | protein | 391 | 40% helix, 16% strand | P06721 |
| B | Cystathionine beta-lyase (EC 4.4.1.8) | protein | 392 | 41% helix, 16% strand | P06721 |
Ligands and binding sites
- P3F · Phosphoric acid mono-(5-hydroxy-6-methyl-4-{[2-(2-trifluoromethyl-benzoylamino)-acetyl]-hydrazonomethyl}-pyridin-3-ylmethyl)ester · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 143 | 0.67 | 0.88 | 26 | empty |
| 2 | 158 | 0.66 | 0.87 | 29 | empty |
| 3 | 200 | 0.63 | 0.83 | 39 | P3F |
| 4 | 196 | 0.59 | 0.81 | 40 | P3F |
| 5 | 57 | 0.51 | 0.87 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 776 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2FQ6 · Cystathionine beta-lyase (cbl) from escherichia coli in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P06721 · AlphaFold monomer V2.0 prediction for cystathionine beta-lyase metc (P06721) · a predicted model of the same protein · chain B 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 P06721
- Elsewhere: RCSB PDB 2FQ6 · PDBe 2FQ6 · UniProt P06721
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