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Crystal structure of lipomyces starkeyi levoglucosan kinase bound to ADP, magnesium and levoglucosan in an alternate orientation.

Analyse Crystal structure of lipomyces starkeyi levoglucosan kinase bound to ADP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5BVC
Type: protein
Length: 433 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Levoglucosan kinase
EC: 2.7.-.-
UniProt: B3VI55
Ligands: ADP, 4PW, MG
Pockets: 6 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Levoglucosan kinase (EC 2.7.-.-)	protein	433	40% helix, 22% strand	B3VI55

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · chains A
4PW · Levoglucosan · ligand · chains A
MG · Magnesium ion · metal · chains A

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	623	0.76	0.82	71	ADP, 4PW, MG
2	54	0.72	0.99	23	empty
3	75	0.38	0.77	17	empty
4	61	0.36	0.79	13	empty
5	58	0.32	0.76	14	empty

Compared structures

5BVC · Crystal structure of Lipomyces starkeyi levoglucosan kinase bound to ADP, magnesium and… · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt B3VI55
Elsewhere: RCSB PDB 5BVC · PDBe 5BVC · UniProt B3VI55

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