MolNFT v1 · #106388 · protein

The structure of GTP-bound SAMHD1

4RXO · Deoxynucleoside triphosphate triphosphohydrolase SAMHD1: “The structure of GTP-bound SAMHD1”. X-ray diffraction, 3 ligands (GTP, ZN, PO4), 20 pockets (best druggability 0.85). MolNFT v1 #106388 on GenesisL1: 3D structure, binding…

PDB: 4RXO
Type: protein
Length: 1,767 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: GTP, ZN, PO4
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 4 distinct chains · 54% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-)	protein	456	53% helix, 12% strand	Q9Y3Z3
B	Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-)	protein	433	55% helix, 12% strand	Q9Y3Z3
C	Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-)	protein	434	55% helix, 12% strand	Q9Y3Z3
D	Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-)	protein	444	53% helix, 12% strand	Q9Y3Z3

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, 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, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	656	0.85	0.89	66	PO4
2	727	0.82	0.86	73	PO4
3	140	0.82	0.98	26	empty
4	1107	0.81	0.82	123	GTP, PO4
5	143	0.81	0.97	25	empty

Interfaces

6 interfaces between chains.

A–B · 1876 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 1876 Å² buried · 20 hydrogen bonds · protein-protein
A–D · 566 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 498 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 43 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

4RXO · The structure of GTP-bound SAMHD1 · 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 Q9Y3Z3
Elsewhere: RCSB PDB 4RXO · PDBe 4RXO · UniProt Q9Y3Z3

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