MolNFT v1 · #167884 · protein

Cryo-EM structure of plasmodium vivax hexokinase (open state)

6VYF · Phosphotransferase: “Cryo-EM structure of plasmodium vivax hexokinase (open state)”. Electron microscopy, 20 pockets (best druggability 0.82). MolNFT v1 #167884 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6VYF
Type: protein
Length: 1,728 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphotransferase
EC: 2.7.1.-
UniProt: A0A1G4HFC9
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · 1 distinct chain · 41% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Phosphotransferase (EC 2.7.1.-)	protein	432	41% helix, 11% strand	A0A1G4HFC9

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1056	0.82	0.83	117	empty
2	1166	0.82	0.83	145	empty
3	479	0.76	0.84	39	empty
4	496	0.75	0.83	51	empty
5	1057	0.70	0.75	110	empty

Interfaces

6 interfaces between chains.

A–B · 720 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 712 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 612 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 612 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 479 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6VYF · Cryo-EM structure of Plasmodium vivax hexokinase (Open state) · 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 A0A1G4HFC9
Elsewhere: RCSB PDB 6VYF · PDBe 6VYF · UniProt A0A1G4HFC9

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