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Staphylopine dehydrogenase in complex with xna

Analyse Staphylopine dehydrogenase in complex with xna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6H3D
Type: protein
Length: 428 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DUF2338 domain-containing protein
UniProt: A0A1K7Y513
Ligands: NDP, DHI
Pockets: 3 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 47% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DUF2338 domain-containing protein	protein	428	47% helix, 16% strand	A0A1K7Y513

Ligands and binding sites

NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
DHI · D-histidine · ligand · chains A
GOL · Glycerol · additive · chains A
PG4 · Tetraethylene glycol · additive · chains A

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	219	0.80	0.93	27	PG4
2	939	0.77	0.79	84	NDP, DHI
3	59	0.28	0.74	15	empty

Compared structures

6H3D · Staphylopine dehydrogenase in complex with xNA · 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 A0A1K7Y513
Elsewhere: RCSB PDB 6H3D · PDBe 6H3D · UniProt A0A1K7Y513

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