Research workbench

PYRI4 in complex with intermolecular diels-alder product

Analyse PYRI4 in complex with intermolecular diels-alder product in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7DVK
Type: protein
Length: 652 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spiro-conjugate synthase
EC: 5.5.1.-
UniProt: K7QVW7
Ligands: HOF
Pockets: 14 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 16% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Spiro-conjugate synthase (EC 5.5.1.-)	protein	163	16% helix, 52% strand	K7QVW7

Ligands and binding sites

HOF · methyl 4-[[(1S,6S)-6-(dimethylcarbamoyl)cyclohex-2-en-1-yl]carbamoyloxymethyl]benzoate · ligand · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 4 copies · chains A, B, C, D

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

Pockets

14 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	210	0.70	0.87	36	GOL
2	191	0.69	0.87	32	GOL
3	264	0.66	0.82	36	HOF
4	239	0.65	0.82	35	HOF
5	271	0.65	0.81	39	HOF

Interfaces

3 interfaces between chains.

C–D · 1518 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1508 Å² buried · 15 hydrogen bonds · protein-protein
A–D · 87 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

7DVK · PyrI4 in complex with intermolecular Diels-Alder product · the same entry in another collection · chain A against A, TM-score 1.00
K7QVW7 · AlphaFold monomer V2.0 prediction for spiro-conjugate synthase (K7QVW7) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 K7QVW7
Elsewhere: RCSB PDB 7DVK · PDBe 7DVK · UniProt K7QVW7

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