MolNFT v1 · #27271 · protein

Crystal structure of stilbene synthase from pinus sylvestris

1XES · Dihydropinosylvin synthase: “Crystal structure of stilbene synthase from pinus sylvestris”. X-ray diffraction, 1 ligand (3IO), 20 pockets (best druggability 0.78). MolNFT v1 #27271 on GenesisL1: 3D structure, binding sites and…

PDB: 1XES
Type: protein
Length: 1,534 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dihydropinosylvin synthase
EC: 2.3.1.-
UniProt: Q02323
Ligands: 3IO
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 41% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Dihydropinosylvin synthase (EC 2.3.1.-)	protein	387	42% helix, 24% strand	Q02323
C	Dihydropinosylvin synthase (EC 2.3.1.-)	protein	378	40% helix, 24% strand	Q02323
D	Dihydropinosylvin synthase (EC 2.3.1.-)	protein	382	41% helix, 24% strand	Q02323

Ligands and binding sites

3IO · 3-(1H-indol-3-yl)-2-oxopropanoic acid · ligand · 4 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	318	0.78	0.89	45	3IO
2	292	0.78	0.89	42	3IO
3	348	0.77	0.87	47	3IO
4	516	0.74	0.82	71	3IO
5	248	0.58	0.79	51	empty

Interfaces

4 interfaces between chains.

A–B · 2963 Å² buried · 64 hydrogen bonds · protein-protein
C–D · 2879 Å² buried · 67 hydrogen bonds · protein-protein
A–C · 320 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 213 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

1XES · Crystal structure of stilbene synthase from Pinus sylvestris · the same entry in another collection · chain C against C, TM-score 1.00
Q02323 · AlphaFold monomer V2.0 prediction for pinosylvin synthase (Q02323) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q02323
Elsewhere: RCSB PDB 1XES · PDBe 1XES · UniProt Q02323

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