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Crystal structure of apo D-serine deaminase from salmonella typhimurium

Analyse Crystal structure of apo D-serine deaminase from salmonella typhimurium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3R0Z
Type: protein
Length: 433 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: D-serine dehydratase
EC: 4.3.1.18
UniProt: Q8ZL08
Ligands: SO4
Pockets: 2 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 53% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	D-serine dehydratase (EC 4.3.1.18)	protein	433	53% helix, 14% strand	Q8ZL08

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains A
EDO · 1,2-ethanediol · additive · 2 copies · chains A

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

Pockets

2 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	372	0.67	0.80	53	SO4
2	50	0.56	0.90	19	empty

Compared structures

3R0Z · Crystal structure of apo D-serine deaminase from Salmonella typhimurium · the same entry in another collection · chain A against A, TM-score 1.00
Q8ZL08 · AlphaFold monomer V2.0 prediction for D-serine dehydratase (Q8ZL08) · a predicted model of the same protein · chain A against A, TM-score 0.97

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q8ZL08
Elsewhere: RCSB PDB 3R0Z · PDBe 3R0Z · UniProt Q8ZL08

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