Research workbench
Crystal structure of DELTA516-525 E201S human cystathionine beta- synthase with adomet
Analyse Crystal structure of DELTA516-525 E201S human cystathionine beta- synthase with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PCU
- Type
- protein
- Length
- 975 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, SAM
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 486 | 38% helix, 15% strand | P35520 |
| B | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 489 | 37% helix, 16% 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
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 138 | 0.81 | 0.98 | 20 | empty |
| 2 | 643 | 0.79 | 0.84 | 72 | PLP |
| 3 | 597 | 0.78 | 0.84 | 71 | SAM |
| 4 | 754 | 0.76 | 0.81 | 64 | empty |
| 5 | 64 | 0.70 | 0.96 | 20 | PLP |
Interfaces
1 interface between chains.
- A–B · 3072 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 4PCU · Crystal structure of delta516-525 E201S human cystathionine beta-synthase with AdoMet · the same entry in another collection · chain B against B, TM-score 1.00
- P35520 · AlphaFold monomer V2.0 prediction for cystathionine beta-synthase (P35520) · a predicted model of the same protein · chain B against A, TM-score 0.87
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 4PCU · PDBe 4PCU · UniProt P35520
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.