MolNFT v1 · #82356 · protein

Crystal structure of MOEO5 soaked with pyrophosphate

3VKC: “Crystal structure of MOEO5 soaked with pyrophosphate”. X-ray diffraction, 3 ligands (FPQ, POP, MG), 5 pockets (best druggability 0.75). MolNFT v1 #82356 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3VKC
Type: protein
Length: 506 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MOEO5
UniProt: A0A011
Ligands: FPQ, POP, MG
Pockets: 5 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	MOEO5	protein	253	41% helix, 19% strand	A0A011

Ligands and binding sites

FPQ · (2R)-3-(phosphonooxy)-2-{[(2Z,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-yl]oxy}propanoic acid · ligand · 2 copies · chains A, B
POP · Pyrophosphate 2- · ligand · chains B
MG · Magnesium ion · metal · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	321	0.75	0.86	36	POP, FPQ
2	338	0.74	0.85	39	FPQ
3	113	0.59	0.85	24	empty
4	118	0.45	0.78	21	empty
5	105	0.42	0.77	21	empty

Interfaces

1 interface between chains.

A–B · 1202 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

3VKC · Crystal structure of MoeO5 soaked with 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 A0A011
Elsewhere: RCSB PDB 3VKC · PDBe 3VKC · UniProt A0A011

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