MolNFT v1 · #34466 · protein

Geranylgeranyl pyrophosphate synthase

2DH4 · YPL069C: “Geranylgeranyl pyrophosphate synthase”. X-ray diffraction, 1 ligand (MG), 8 pockets (best druggability 0.82). MolNFT v1 #34466 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2DH4
Type: protein
Length: 652 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: YPL069C
EC: 2.5.1.29
UniProt: Q12051
Ligands: MG
Pockets: 8 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 74% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	YPL069C (EC 2.5.1.29)	protein	326	74% helix, 1% strand	Q12051

Ligands and binding sites

MG · Magnesium ion · metal · 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	652	0.82	0.86	60	MG
2	530	0.76	0.84	47	MG
3	132	0.58	0.83	17	empty
4	116	0.57	0.83	14	empty
5	112	0.41	0.76	20	empty

Interfaces

1 interface between chains.

A–B · 3544 Å² buried · 35 hydrogen bonds · protein-protein

Compared structures

2DH4 · Geranylgeranyl pyrophosphate synthase · the same entry in another collection · chain A against A, TM-score 1.00
Q12051 · AlphaFold monomer V2.0 prediction for geranylgeranyl pyrophosphate synthase (Q12051) · a predicted model of the same protein · chain B against A, TM-score 0.94

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 Q12051
Elsewhere: RCSB PDB 2DH4 · PDBe 2DH4 · UniProt Q12051

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