MolNFT v1 · #98142 · protein
Crystal structure of DELTA516-525 human cystathionine beta-synthase containing C-terminal 6XHIS-tag
4L0D: “Crystal structure of DELTA516-525 human cystathionine beta-synthase containing C-terminal 6XHIS-tag”. X-ray diffraction, 2 ligands (PLP, HEM), 15 pockets (best druggability 0.78). MolNFT v1 #98142 on GenesisL1: 3D structure, binding…
- PDB
- 4L0D
- Type
- protein
- Length
- 992 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
- PLP, HEM
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 496 | 38% helix, 16% strand | P35520 |
| B | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 496 | 40% helix, 16% strand | P35520 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 117 | 0.78 | 0.97 | 20 | empty |
| 2 | 937 | 0.75 | 0.79 | 66 | empty |
| 3 | 69 | 0.73 | 0.98 | 26 | PLP |
| 4 | 65 | 0.73 | 0.99 | 26 | PLP |
| 5 | 404 | 0.73 | 0.84 | 46 | empty |
Interfaces
1 interface between chains.
- A–B · 3858 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 4L0D · Crystal structure of delta516-525 human cystathionine beta-synthase containing C-terminal… · 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 B against A, TM-score 0.74
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 4L0D · PDBe 4L0D · UniProt P35520
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