MolNFT v1 · #5051 · protein

K15M mutant of shikimate kinase from erwinia chrysanthemi

1E6C: “K15M mutant of shikimate kinase from erwinia chrysanthemi”. X-ray diffraction, 2 ligands (PO4, CL), 3 pockets (best druggability 0.82). MolNFT v1 #5051 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1E6C
Type: protein
Length: 340 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Shikimate kinase
EC: 2.7.1.71
UniProt: P10880
Ligands: PO4, CL
Pockets: 3 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 61% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Shikimate kinase (EC 2.7.1.71)	protein	170	61% helix, 13% strand	P10880

Ligands and binding sites

PO4 · Phosphate ion · ion · 2 copies · chains A, B
CL · Chloride ion · ion · 2 copies · chains A, B
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 5 copies · chains A, B
MRD · (4R)-2-methylpentane-2,4-diol · additive · chains A, B

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

Pockets

3 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	1155	0.82	0.83	81	PO4, CL, MPD, MRD
2	368	0.69	0.82	48	MPD
3	61	0.32	0.76	12	empty

Interfaces

1 interface between chains.

A–B · 1471 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

1E6C · K15M mutant of shikimate kinase from erwinia chrysanthemi · the same entry in another collection · chain A against A, TM-score 1.00
P10880 · AlphaFold monomer V2.0 prediction for shikimate kinase 2 (P10880) · a predicted model of the same protein · chain A against A, TM-score 0.83

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 P10880
Elsewhere: RCSB PDB 1E6C · PDBe 1E6C · UniProt P10880

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