MolNFT v1 · #14305 · protein
Cystathionine-beta synthase: reduced vicinal thiols
1M54 · Cystathionine beta-synthase: “Cystathionine-beta synthase: reduced vicinal thiols”. X-ray diffraction, 2 ligands (PLP, HEM), 20 pockets (best druggability 0.85). MolNFT v1 #14305 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1M54
- Type
- protein
- Length
- 2,082 residues
- Chains
- 6
- 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
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 32% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 352 | 29% helix, 14% strand | P35520 |
| B | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 347 | 33% helix, 14% strand | P35520 |
| C, D | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 346 | 35% helix, 13% strand | P35520 |
| E | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 347 | 31% helix, 14% strand | P35520 |
| F | Cystathionine beta-synthase (EC 4.2.1.22) | protein | 344 | 32% helix, 14% strand | P35520 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 6 copies · chains A, B, C, D, E, F
- HEM · Protoporphyrin IX containing Fe · ligand · 6 copies · chains A, F, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 796 | 0.85 | 0.88 | 103 | empty |
| 2 | 659 | 0.83 | 0.88 | 80 | empty |
| 3 | 179 | 0.82 | 0.97 | 27 | empty |
| 4 | 150 | 0.80 | 0.97 | 22 | empty |
| 5 | 147 | 0.80 | 0.96 | 23 | empty |
Interfaces
10 interfaces between chains.
- E–F · 2148 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1966 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1957 Ų buried · 18 hydrogen bonds · protein-protein
- D–F · 715 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 674 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 cofactor (pyridoxal phosphate Schiff base).
Compared structures
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 1M54 · PDBe 1M54 · UniProt P35520
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