MolNFT v1 · #67613 · protein

Crystal structure of a geranyltranstransferase from the methanosarcina mazei

3IPI: “Crystal structure of a geranyltranstransferase from the methanosarcina mazei”. X-ray diffraction, 2 pockets (best druggability 0.68). MolNFT v1 #67613 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3IPI
Type: protein
Length: 268 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Geranyltranstransferase
EC: 2.5.1.-
UniProt: Q8PYS1
Pockets: 2 · best druggability 0.68

Structure

x-ray diffraction · 1 distinct chain · 80% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Geranyltranstransferase (EC 2.5.1.-)	protein	268	80% helix, 0% strand	Q8PYS1

Ligands and binding sites

MLA · Malonic acid · additive · 6 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	500	0.68	0.79	69	MLA
2	68	0.36	0.77	17	empty

Modifications

Observed in the structure: 7 modified (engineered).

Compared structures

3IPI · Crystal Structure of a Geranyltranstransferase from the Methanosarcina mazei · the same entry in another collection · chain A against A, TM-score 1.00
Q8PYS1 · AlphaFold monomer V2.0 prediction for geranylfarnesyl diphosphate synthase (Q8PYS1) · a predicted model of the same protein · chain A 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 Q8PYS1
Elsewhere: RCSB PDB 3IPI · PDBe 3IPI · UniProt Q8PYS1

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