MolNFT v1 · #82610 · protein
Crystal structure of the K127A mutant of O-phosphoserine sulfhydrylase complexed with external schiff base of pyridoxal 5'-phosphate with O- acetyl-L-serine
3VSD · Protein cyso: “Crystal structure of the K127A mutant of O-phosphoserine sulfhydrylase complexed with external schiff base of…”. X-ray diffraction, 2 ligands (PLP, OAS), 8 pockets (best druggability 0.75). MolNFT v1 #82610 on…
- PDB
- 3VSD
- 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, OAS
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 19% 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 | 47% helix, 19% strand | Q9YBL2 |
| B | Protein cyso (EC 4.2.1.22, 2.5.1.47, 2.5.1.65) | protein | 383 | 45% helix, 19% strand | Q9YBL2 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- OAS · O-acetylserine · 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
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 322 | 0.75 | 0.87 | 49 | PLP, OAS |
| 2 | 300 | 0.75 | 0.87 | 47 | PLP, OAS |
| 3 | 57 | 0.74 | 0.99 | 20 | MPD |
| 4 | 298 | 0.59 | 0.78 | 30 | empty |
| 5 | 222 | 0.54 | 0.78 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 2617 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3VSD · Crystal Structure of the K127A Mutant of O-Phosphoserine Sulfhydrylase Complexed with… · the same entry in another collection · chain B against B, TM-score 1.00
- Q9YBL2 · AlphaFold monomer V2.0 prediction for protein cyso (Q9YBL2) · a predicted model of the same protein · chain B against A, TM-score 1.00
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 3VSD · PDBe 3VSD · UniProt Q9YBL2
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