MolNFT v1 · #114032 · protein

Structure of the prenyltransferase MOEN5 in complex with geranyl pyrophosphate

5B00: “Structure of the prenyltransferase MOEN5 in complex with geranyl pyrophosphate”. X-ray diffraction, 1 ligand (GPP), 7 pockets (best druggability 0.77). MolNFT v1 #114032 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5B00
Type: protein
Length: 783 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MOEN5
UniProt: A0A010
Ligands: GPP
Pockets: 7 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 72% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	MOEN5	protein	261	72% helix, 0% strand	A0A010

Ligands and binding sites

GPP · Geranyl diphosphate · ligand · 3 copies · chains A, B, C

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

Pockets

7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	747	0.77	0.81	63	GPP
2	746	0.77	0.81	71	GPP
3	770	0.76	0.81	61	GPP
4	50	0.71	0.98	18	empty
5	174	0.58	0.81	34	empty

Interfaces

2 interfaces between chains.

B–C · 1810 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 543 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

5B00 · Structure of the prenyltransferase MoeN5 in complex with geranyl pyrophosphate · 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 A0A010
Elsewhere: RCSB PDB 5B00 · PDBe 5B00 · UniProt A0A010

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