MolNFT v1 · #109913 · protein

Structure of C. elegans pch-2

4XGU · Putative pachytene checkpoint protein 2: “Structure of C. elegans pch-2”. X-ray diffraction, 2 ligands (ADP, SO4), 20 pockets (best druggability 0.85). MolNFT v1 #109913 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4XGU
Type: protein
Length: 2,264 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative pachytene checkpoint protein 2
UniProt: Q09535
Ligands: ADP, SO4
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 6 distinct chains · 43% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative pachytene checkpoint protein 2	protein	376	43% helix, 16% strand	Q09535
B	Putative pachytene checkpoint protein 2	protein	382	44% helix, 15% strand	Q09535
C	Putative pachytene checkpoint protein 2	protein	374	42% helix, 17% strand	Q09535
D	Putative pachytene checkpoint protein 2	protein	377	43% helix, 16% strand	Q09535
E	Putative pachytene checkpoint protein 2	protein	379	42% helix, 15% strand	Q09535
F	Putative pachytene checkpoint protein 2	protein	376	44% helix, 17% strand	Q09535

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains B, C, E, F
SO4 · Sulfate ion · ion · 7 copies · chains A, C, D, E, F

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	1002	0.85	0.86	91	ADP
2	988	0.84	0.85	91	SO4
3	719	0.82	0.85	55	ADP
4	985	0.81	0.82	71	SO4
5	730	0.69	0.77	65	SO4

Interfaces

7 interfaces between chains.

B–C · 1469 Å² buried · 9 hydrogen bonds · protein-protein
D–E · 1447 Å² buried · 9 hydrogen bonds · protein-protein
E–F · 1399 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 1234 Å² buried · 3 hydrogen bonds · protein-protein
A–F · 1041 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

4XGU · Structure of C. elegans PCH-2 · the same entry in another collection · chain F against F, TM-score 1.00
Q09535 · AlphaFold monomer V2.0 prediction for putative pachytene checkpoint protein 2 (Q09535) · a predicted model of the same protein · chain E against A, TM-score 0.97

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 Q09535
Elsewhere: RCSB PDB 4XGU · PDBe 4XGU · UniProt Q09535

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.