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2-keto-3-deoxygluconate kinase from thermus thermophilus with bound ATP

Analyse 2-keto-3-deoxygluconate kinase from thermus thermophilus with bound ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1V1B
Type: protein
Length: 1,200 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2-keto-3-deoxygluconate kinase
Ligands: ATP
Pockets: 11 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	2-keto-3-deoxygluconate kinase	protein	300	39% helix, 21% strand	—

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	605	0.71	0.79	53	ATP
2	533	0.69	0.79	55	ATP
3	557	0.69	0.78	54	ATP
4	501	0.67	0.78	53	ATP
5	379	0.61	0.77	40	empty

Interfaces

3 interfaces between chains.

A–B · 1184 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 1170 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 216 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

1V1B · 2-keto-3-deoxygluconate kinase from thermus thermophilus with bound ATP · 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
Elsewhere: RCSB PDB 1V1B · PDBe 1V1B

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