MolNFT v1 · #24650 · protein

2-keto-3-deoxygluconate kinase from thermus thermophilus (crystal form 2)

1V1S: “2-keto-3-deoxygluconate kinase from thermus thermophilus (crystal form 2)”. X-ray diffraction, 20 pockets (best druggability 0.71). MolNFT v1 #24650 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1V1S
Type: protein
Length: 1,806 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2-keto-3-deoxygluconate kinase
Pockets: 20 · best druggability 0.71

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	2-keto-3-deoxygluconate kinase	protein	301	40% helix, 22% strand	—

Pockets

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	572	0.71	0.80	62	empty
2	569	0.71	0.79	59	empty
3	598	0.70	0.79	61	empty
4	564	0.70	0.79	55	empty
5	588	0.70	0.79	56	empty

Interfaces

6 interfaces between chains.

C–D · 1411 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1334 Å² buried · 20 hydrogen bonds · protein-protein
E–F · 1273 Å² buried · 19 hydrogen bonds · protein-protein
C–F · 482 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 292 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

1V1S · 2-keto-3-deoxygluconate kinase from thermus thermophilus (crystal form 2) · 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 1V1S · PDBe 1V1S

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