MolNFT v1 · #144795 · protein

Staphylopine dehydrogenase (saodh) - NADP+ bound

6C4T: “Staphylopine dehydrogenase (saodh) - NADP+ bound”. X-ray diffraction, 1 ligand (NA7), 3 pockets (best druggability 0.80). MolNFT v1 #144795 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6C4T
Type: protein
Length: 428 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Staphylopine dehydrogenase
UniProt: A0A1Q4GXD5
Ligands: NA7
Pockets: 3 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Staphylopine dehydrogenase	protein	428	45% helix, 16% strand	A0A1Q4GXD5

Ligands and binding sites

NA7 · [(2R,3R,4R,5R)-5-(6-amino-9H-purin-9-yl)-3-hydroxy-4-(phosphonooxy)tetrahydrofuran-2-yl]methyl [(2R,3S,4S)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate · ligand · chains A
GOL · Glycerol · 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	221	0.80	0.93	27	empty
2	1128	0.77	0.79	95	NA7
3	58	0.26	0.72	17	empty

Compared structures

6C4T · Staphylopine dehydrogenase (SaODH) - NADP+ bound · 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 A0A1Q4GXD5
Elsewhere: RCSB PDB 6C4T · PDBe 6C4T · UniProt A0A1Q4GXD5

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