MolNFT v1 · #25193 · protein

Crystal structure of shikimate kinase

1VIA: “Crystal structure of shikimate kinase”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.62). MolNFT v1 #25193 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1VIA
Type: protein
Length: 315 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Shikimate kinase
EC: 2.7.1.71
UniProt: Q9PIB5
Ligands: SO4
Pockets: 5 · best druggability 0.62

Structure

x-ray diffraction · 2 distinct chains · 57% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Shikimate kinase (EC 2.7.1.71)	protein	161	55% helix, 14% strand	Q9PIB5
B	Shikimate kinase (EC 2.7.1.71)	protein	154	58% helix, 14% strand	Q9PIB5

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	227	0.62	0.81	25	SO4
2	190	0.45	0.74	30	SO4
3	103	0.43	0.78	19	empty
4	63	0.40	0.80	14	empty
5	65	0.28	0.72	12	empty

Interfaces

1 interface between chains.

A–B · 1175 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (engineered).

Compared structures

1VIA · Crystal structure of shikimate kinase · 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 Q9PIB5
Elsewhere: RCSB PDB 1VIA · PDBe 1VIA · UniProt Q9PIB5

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