MolNFT v1 · #172070 · protein

Crystal structure of chaetomium thermophilum glycerol kinase in complex with glycerol in P21212 space group

6ZQ6 · Glycerol kinase-like protein: “Crystal structure of chaetomium thermophilum glycerol kinase in complex with glycerol in P21212 space group”. X-ray diffraction, 20 pockets (best druggability 0.79). MolNFT v1 #172070 on GenesisL1: 3D…

PDB: 6ZQ6
Type: protein
Length: 2,038 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycerol kinase-like protein
UniProt: G0SAG9
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 38% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glycerol kinase-like protein	protein	510	38% helix, 22% strand	G0SAG9
B	Glycerol kinase-like protein	protein	510	37% helix, 22% strand	G0SAG9
C, D	Glycerol kinase-like protein	protein	509	38% helix, 21% strand	G0SAG9

Ligands and binding sites

GOL · Glycerol · additive · 5 copies · chains A, B, C, D
ACT · Acetate ion · additive · chains C

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

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1035	0.79	0.81	98	GOL
2	933	0.77	0.80	97	GOL
3	935	0.75	0.79	60	empty
4	564	0.70	0.79	49	GOL
5	527	0.69	0.79	54	GOL

Interfaces

5 interfaces between chains.

B–C · 383 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 289 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 254 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 248 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 240 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6ZQ6 · Crystal structure of Chaetomium thermophilum Glycerol Kinase in complex with glycerol in… · 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 G0SAG9
Elsewhere: RCSB PDB 6ZQ6 · PDBe 6ZQ6 · UniProt G0SAG9

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