MolNFT v1 · #114141 · protein
Crystal structure of O-phoshoserine sulfhydrylase from aeropyrum pernix in complexed with the alpha-aminoacrylate intermediate
5B3A · Protein cyso: “Crystal structure of O-phoshoserine sulfhydrylase from aeropyrum pernix in complexed with the…”. X-ray diffraction, 1 ligand (0JO), 8 pockets (best druggability 0.74). MolNFT v1 #114141 on GenesisL1: 3D structure…
- PDB
- 5B3A
- 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
- 0JO
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 44% 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 | 43% helix, 19% strand | Q9YBL2 |
| B | Protein cyso (EC 4.2.1.22, 2.5.1.47, 2.5.1.65) | protein | 383 | 44% helix, 18% strand | Q9YBL2 |
Ligands and binding sites
- 0JO · 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid · ligand · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · 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 | 58 | 0.74 | 0.99 | 19 | MPD |
| 2 | 287 | 0.71 | 0.85 | 47 | 0JO |
| 3 | 262 | 0.70 | 0.85 | 42 | 0JO |
| 4 | 280 | 0.58 | 0.78 | 34 | empty |
| 5 | 227 | 0.54 | 0.78 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 2653 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 5B3A · Crystal Structure of O-Phoshoserine Sulfhydrylase from Aeropyrum pernix in Complexed with… · the same entry in another collection · chain A against A, 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 5B3A · PDBe 5B3A · UniProt Q9YBL2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.