MolNFT v2 · #147821 · protein

SAMHD1 Bound to Gemcitabine-TP in the Catalytic Pocket

6DW5: “SAMHD1 Bound to Gemcitabine-TP in the Catalytic Pocket”. X-ray diffraction at 1.93, 6 ligands (GTF, GTP, DTP). MolNFT v2 #147821 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6DW5
Type: protein
Length: 1,910 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.93
Source: Homo sapiens
UniProt: Q9Y3Z3
Ligands: GTF, GTP, DTP, MG, NA, NI

Structure

x-ray diffraction · resolution 1.93 · 3 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	—	protein	468	—	Q9Y3Z3
B	—	protein	480	—	Q9Y3Z3
C, D	—	protein	481	—	Q9Y3Z3

Ligands and binding sites

GTF · 2'-deoxy-2',2'-difluorocytidine 5'-(tetrahydrogen triphosphate) · ligand · 4 copies · chains A, B, C, D
GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains A, C, D, B
DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 10 copies · chains A, B, C, D
NA · Sodium ion · metal · 4 copies · chains A, B, C
NI · Nickel (II) ion · metal · chains B, C

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

Compared structures

6DW5 · SAMHD1 bound to gemcitabine-tp in the catalytic pocket · the same entry in another collection · chain A against A, TM-score 1.00
Q9Y3Z3 · AlphaFold monomer V2.0 prediction for deoxynucleoside triphosphate triphosphohydrolase… · a predicted model of the same protein · chain B 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 Q9Y3Z3
Elsewhere: RCSB PDB 6DW5 · PDBe 6DW5 · UniProt Q9Y3Z3

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