Research workbench
Crystal structure of the O-phosphoserine sulfhydrylase from aeropyrum pernix complexed with O-acetylserine
Analyse Crystal structure of the O-phosphoserine sulfhydrylase from aeropyrum pernix… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6L0R
- Type
- protein
- Length
- 1,528 residues
- Chains
- 4
- 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
- E1R
- Pockets
- 19 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Protein cyso (EC 4.2.1.22, 2.5.1.47, 2.5.1.65) | protein | 382 | 46% helix, 21% strand | Q9YBL2 |
Ligands and binding sites
- E1R · (2S)-3-acetyloxy-2-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]propanoic acid · ligand · 4 copies · chains A, B, C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 953 | 0.79 | 0.81 | 121 | empty |
| 2 | 325 | 0.76 | 0.88 | 47 | E1R |
| 3 | 296 | 0.75 | 0.88 | 46 | E1R |
| 4 | 465 | 0.75 | 0.84 | 69 | E1R |
| 5 | 338 | 0.74 | 0.86 | 52 | E1R |
Interfaces
5 interfaces between chains.
- C–D · 2643 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2598 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 688 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 205 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 194 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6L0R · Crystal Structure of the O-Phosphoserine Sulfhydrylase from Aeropyrum pernix Complexed… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9YBL2 · AlphaFold monomer V2.0 prediction for protein cyso (Q9YBL2) · a predicted model of the same protein · chain D 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 6L0R · PDBe 6L0R · UniProt Q9YBL2
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