MolNFT v1 · #155222 · protein
Crystal structure of the O-phosphoserine sulfhydrylase from aeropyrum pernix complexed with O-phosphoserine
6L0P · Protein cyso: “Crystal structure of the O-phosphoserine sulfhydrylase from aeropyrum pernix complexed with O-phosphoserine”. X-ray diffraction, 1 ligand (E1U), 17 pockets (best druggability 0.80). MolNFT v1 #155222 on GenesisL1: 3D…
- PDB
- 6L0P
- 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
- E1U
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 45% 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 | 45% helix, 21% strand | Q9YBL2 |
Ligands and binding sites
- E1U · (2S)-2-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-3-phosphonooxy-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
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1156 | 0.80 | 0.81 | 140 | empty |
| 2 | 313 | 0.76 | 0.88 | 48 | E1U |
| 3 | 342 | 0.76 | 0.87 | 50 | E1U |
| 4 | 326 | 0.75 | 0.87 | 48 | E1U |
| 5 | 331 | 0.75 | 0.87 | 49 | E1U |
Interfaces
5 interfaces between chains.
- C–D · 2629 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2627 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 671 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 206 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 186 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6L0P · 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 6L0P · PDBe 6L0P · UniProt Q9YBL2
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