MolNFT v1 · #24634 · protein

2-keto-3-deoxygluconate kinase from thermus thermophilus

1V19: “2-keto-3-deoxygluconate kinase from thermus thermophilus”. X-ray diffraction, 6 pockets (best druggability 0.70). MolNFT v1 #24634 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1V19
Type: protein
Length: 602 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2-keto-3-deoxygluconate kinase
Pockets: 6 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	2-keto-3-deoxygluconate kinase	protein	301	39% helix, 24% strand	—

Ligands and binding sites

DIO · 1,4-diethylene dioxide · additive · chains A, B

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	566	0.70	0.79	58	empty
2	592	0.69	0.78	61	empty
3	184	0.45	0.74	31	DIO
4	81	0.37	0.77	13	empty
5	86	0.36	0.75	12	empty

Interfaces

1 interface between chains.

A–B · 1184 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

1V19 · 2-keto-3-deoxygluconate kinase from thermus thermophilus · 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 1V19 · PDBe 1V19

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