MolNFT v1 · #82607 · protein
Crystal structure of O-phosphoserine sulfhydrylase without acetate
3VSA · Protein cyso: “Crystal structure of O-phosphoserine sulfhydrylase without acetate”. X-ray diffraction, 1 ligand (PLP), 10 pockets (best druggability 0.75). MolNFT v1 #82607 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3VSA
- Type
- protein
- Length
- 765 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein cyso
- EC
- 4.2.1.22, 2.5.1.47, 2.5.1.65
- UniProt
- Q9YBL2
- Ligands
- PLP
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein cyso (EC 4.2.1.22, 2.5.1.47, 2.5.1.65) | protein | 382 | 45% helix, 20% strand | Q9YBL2 |
| B | Protein cyso (EC 4.2.1.22, 2.5.1.47, 2.5.1.65) | protein | 383 | 46% helix, 19% strand | Q9YBL2 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.75 | 1.00 | 20 | MPD |
| 2 | 58 | 0.70 | 0.97 | 27 | PLP |
| 3 | 51 | 0.68 | 0.97 | 24 | PLP |
| 4 | 207 | 0.60 | 0.81 | 30 | empty |
| 5 | 195 | 0.60 | 0.82 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 2598 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor, 2 disulfide (pyridoxal phosphate Schiff base, disulfide).
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 Q9YBL2
- Elsewhere: RCSB PDB 3VSA · PDBe 3VSA · UniProt Q9YBL2
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