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Crystal structure of shikimate dehydrogenase from staphylococcus epidermidis complexed with shikimate

Analyse Crystal structure of shikimate dehydrogenase from staphylococcus epidermidis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3DOO
Type: protein
Length: 258 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Shikimate dehydrogenase
EC: 1.1.1.25
UniProt: Q5HNV1
Ligands: SKM
Pockets: 1 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Shikimate dehydrogenase (EC 1.1.1.25)	protein	258	41% helix, 19% strand	Q5HNV1

Ligands and binding sites

SKM · (3R,4S,5R)-3,4,5-trihydroxycyclohex-1-ene-1-carboxylic acid · ligand · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	339	0.59	0.77	34	SKM

Compared structures

3DOO · Crystal structure of shikimate dehydrogenase from Staphylococcus epidermidis complexed… · the same entry in another collection · chain A against A, TM-score 1.00
Q5HNV1 · AlphaFold monomer V2.0 prediction for shikimate dehydrogenase (NADP(+)) (Q5HNV1) · a predicted model of the same protein · chain A against A, TM-score 0.91

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 Q5HNV1
Elsewhere: RCSB PDB 3DOO · PDBe 3DOO · UniProt Q5HNV1

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