MolNFT v1 · #47513 · protein
Crystal structure of marchantia polymorpha stilbenecarboxylate synthase 2 (STCS2)
2P0U: “Crystal structure of marchantia polymorpha stilbenecarboxylate synthase 2 (STCS2)”. X-ray diffraction, 2 ligands (NI, SO4), 6 pockets (best druggability 0.78). MolNFT v1 #47513 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2P0U
- Type
- protein
- Length
- 802 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Stilbenecarboxylate synthase 2
- EC
- 2.3.1.74
- UniProt
- Q5I6Y1
- Ligands
- NI, SO4
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Stilbenecarboxylate synthase 2 (EC 2.3.1.74) | protein | 403 | 40% helix, 23% strand | Q5I6Y1 |
| B | Stilbenecarboxylate synthase 2 (EC 2.3.1.74) | protein | 399 | 40% helix, 24% strand | Q5I6Y1 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · chains B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 388 | 0.78 | 0.87 | 56 | empty |
| 2 | 308 | 0.75 | 0.87 | 55 | empty |
| 3 | 110 | 0.48 | 0.80 | 28 | empty |
| 4 | 113 | 0.45 | 0.78 | 27 | empty |
| 5 | 80 | 0.42 | 0.80 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 3234 Ų buried · 53 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 2P0U · crystal structure of Marchantia polymorpha stilbenecarboxylate synthase 2 (STCS2) · the same entry in another collection · chain A 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 Q5I6Y1
- Elsewhere: RCSB PDB 2P0U · PDBe 2P0U · UniProt Q5I6Y1
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