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Structure of C. elegans ZK177.8, SAMHD1 ortholog

Analyse Structure of C. elegans ZK177.8, SAMHD1 ortholog in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6PWY
Type: protein
Length: 2,033 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ZK177.8
UniProt: Q09374
Ligands: DTP, GTP, MG
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 3 distinct chains · 56% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ZK177.8	protein	504	56% helix, 12% strand	Q09374
B, C	ZK177.8	protein	513	56% helix, 11% strand	Q09374
D	ZK177.8	protein	503	56% helix, 12% strand	Q09374

Ligands and binding sites

DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 8 copies · chains A, B, D, C
GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains A, B, D, C
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
SIN · Succinic acid · additive · 6 copies · chains A, B, D, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	875	0.89	0.91	122	MG, DTP, GTP
2	932	0.88	0.91	129	DTP, MG, GTP
3	99	0.77	0.98	21	empty
4	672	0.70	0.78	56	DTP
5	647	0.70	0.78	60	DTP, SIN

Interfaces

6 interfaces between chains.

B–C · 2073 Å² buried · 20 hydrogen bonds · protein-protein
A–D · 1939 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1781 Å² buried · 17 hydrogen bonds · protein-protein
D–C · 1772 Å² buried · 20 hydrogen bonds · protein-protein
B–D · 544 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6PWY · Structure of C. elegans ZK177.8, SAMHD1 ortholog · the same entry in another collection · chain A against A, TM-score 1.00
Q09374 · AlphaFold monomer V2.0 prediction for uncharacterized protein ZK177.8 (Q09374) · a predicted model of the same protein · 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 Q09374
Elsewhere: RCSB PDB 6PWY · PDBe 6PWY · UniProt Q09374

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