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SAMHD1 bound to clofarabine-tp in the catalytic pocket and allosteric pocket

Analyse SAMHD1 bound to clofarabine-tp in the catalytic pocket and allosteric pocket in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6DWD
Type: protein
Length: 1,916 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
UniProt: Q9Y3Z3
Ligands: HDV, GTP, TCE, NA, MG, PO4

Structure

x-ray diffraction · 3 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, B	—	protein	482	—	Q9Y3Z3
C	—	protein	483	—	Q9Y3Z3
A	—	protein	469	—	Q9Y3Z3

Ligands and binding sites

HDV · 9-{2-deoxy-2-fluoro-5-O-[(R)-hydroxy{[(s)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}-2-methyl-9H-purin-6-amine · ligand · 8 copies · chains D, C, B, A
GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains D, B, A, C
TCE · 3,3',3''-phosphanetriyltripropanoic acid · ligand · chains A
NA · Sodium ion · metal · 23 copies · chains D, B, C, A
MG · Magnesium ion · metal · 10 copies · chains D, C, B, A
PO4 · Phosphate ion · ion · chains C
SIN · Succinic acid · additive · 2 copies · chains D, B

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

Compared structures

6DWD · SAMHD1 Bound to Clofarabine-TP in the Catalytic Pocket and Allosteric Pocket · the same entry in another collection · chain D against D, 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 Q9Y3Z3
Elsewhere: RCSB PDB 6DWD · PDBe 6DWD · UniProt Q9Y3Z3

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