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Crystal structure of human cystathionine beta-synthase (DELTA516-525) at 2.0 ångström resolution
Analyse Crystal structure of human cystathionine beta-synthase (DELTA516-525) at 2.0… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4COO
- Type
- protein
- Length
- 980 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cystathionine beta-synthase
- EC
- 4.2.1.22
- UniProt
- P35520
- Ligands
- HEM, PLP, NA
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 493 | 39% helix, 17% strand | P35520 |
| B | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 487 | 37% helix, 17% strand | P35520 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
- ACT · Acetate ion · additive · 5 copies · chains A, B
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 138 | 0.81 | 0.98 | 20 | empty |
| 2 | 927 | 0.75 | 0.78 | 69 | empty |
| 3 | 261 | 0.73 | 0.87 | 40 | EDO, NA |
| 4 | 63 | 0.72 | 0.98 | 28 | PLP |
| 5 | 286 | 0.72 | 0.86 | 39 | NA |
Interfaces
1 interface between chains.
- A–B · 3715 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 4COO · Crystal structure of human cystathionine beta-synthase (delta516-525) at 2.0 angstrom… · the same entry in another collection · chain A against A, TM-score 1.00
- P35520 · AlphaFold monomer V2.0 prediction for cystathionine beta-synthase (P35520) · a predicted model of the same protein · chain A against A, TM-score 0.75
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 P35520
- Elsewhere: RCSB PDB 4COO · PDBe 4COO · UniProt P35520
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