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SAMHD1 without catalytic nucleotides

Analyse SAMHD1 without catalytic nucleotides in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6DW7
Type: protein
Length: 1,923 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
EC: 3.1.5.-
UniProt: Q9Y3Z3
Ligands: DTP, GTP, GLY, MG, NA, PO4
Pockets: 20 · best druggability 0.90

Structure

x-ray diffraction · 2 distinct chains · 53% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-)	protein	480	53% helix, 13% strand	Q9Y3Z3
B, C, D	Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-)	protein	481	53% helix, 13% strand	Q9Y3Z3

Ligands and binding sites

DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 4 copies · chains A, B, C, D
GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains A, B, D, C
GLY · Glycine · ligand · 2 copies · chains A, C
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
NA · Sodium ion · metal · 3 copies · chains A, C
PO4 · Phosphate ion · ion · chains D

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

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1062	0.90	0.92	159	GTP, DTP, MG
2	987	0.90	0.92	155	DTP, MG, GTP
3	137	0.82	0.98	26	empty
4	133	0.82	0.98	26	empty
5	338	0.74	0.86	34	empty

Interfaces

6 interfaces between chains.

A–C · 2233 Å² buried · 34 hydrogen bonds · protein-protein
B–D · 2207 Å² buried · 31 hydrogen bonds · protein-protein
A–D · 1973 Å² buried · 22 hydrogen bonds · protein-protein
B–C · 1972 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 563 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

6DW7 · SAMHD1 without Catalytic Nucleotides · the same entry in another collection · chain D against D, TM-score 1.00
Q9Y3Z3 · AlphaFold monomer V2.0 prediction for deoxynucleoside triphosphate triphosphohydrolase… · a predicted model of the same protein · chain C 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 6DW7 · PDBe 6DW7 · UniProt Q9Y3Z3

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