MolNFT v1 · #82357 · protein

Crystal structure of MOEO5 soaked with 3-phosphoglycerate

3VKD: “Crystal structure of MOEO5 soaked with 3-phosphoglycerate”. X-ray diffraction, 3 ligands (FPQ, MG, PO4), 7 pockets (best druggability 0.74). MolNFT v1 #82357 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3VKD
Type: protein
Length: 505 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MOEO5
UniProt: A0A011
Ligands: FPQ, MG, PO4
Pockets: 7 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MOEO5	protein	253	41% helix, 19% strand	A0A011
B	MOEO5	protein	252	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
MG · Magnesium ion · metal · 2 copies · chains A, B
PO4 · Phosphate ion · ion · chains B

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

Pockets

7 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	312	0.74	0.86	33	PO4, FPQ
2	319	0.74	0.86	36	FPQ
3	136	0.55	0.82	22	empty
4	109	0.47	0.80	22	empty
5	81	0.41	0.78	20	empty

Interfaces

1 interface between chains.

A–B · 1186 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

3VKD · Crystal structure of MoeO5 soaked with 3-phosphoglycerate · the same entry in another collection · chain B against B, 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 3VKD · PDBe 3VKD · UniProt A0A011

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