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Sy-crte ipp structure

Analyse Sy-crte ipp structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7MY0
Type: protein
Length: 574 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Geranylgeranyl pyrophosphate synthase
UniProt: P72683
Ligands: IPE, MG
Pockets: 4 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 77% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Geranylgeranyl pyrophosphate synthase	protein	286	77% helix, 1% strand	P72683
B	Geranylgeranyl pyrophosphate synthase	protein	288	77% helix, 1% strand	P72683

Ligands and binding sites

IPE · 3-methylbut-3-enyl trihydrogen diphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 8 copies · chains A, B
GOL · Glycerol · additive · chains A

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	597	0.70	0.79	50	IPE, MG
2	577	0.70	0.79	55	IPE, MG
3	54	0.43	0.82	14	empty
4	63	0.39	0.79	13	empty

Interfaces

1 interface between chains.

A–B · 2018 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

7MY0 · Sy-CrtE IPP structure · 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 P72683
Elsewhere: RCSB PDB 7MY0 · PDBe 7MY0 · UniProt P72683

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