MolNFT v1 · #129913 · protein

Crystal structure of the catalytic core of a rhodopsin-guanylyl cyclase with converted specificity in complex with atpalphas

5OYH · Nucleotide cyclase: “Crystal structure of the catalytic core of a rhodopsin-guanylyl cyclase with converted specificity in complex…”. X-ray diffraction, 2 ligands (T99, CA), 20 pockets (best druggability 0.86). MolNFT v1 #129913 on…

PDB: 5OYH
Type: protein
Length: 2,928 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleotide cyclase
UniProt: A0A1Y2HEJ3
Ligands: T99, CA
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 9 distinct chains · 36% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nucleotide cyclase	protein	184	35% helix, 36% strand	A0A1Y2HEJ3
B, C	Nucleotide cyclase	protein	184	35% helix, 36% strand	A0A1Y2HEJ3
D, F, G, H, J, L	Nucleotide cyclase	protein	185	35% helix, 37% strand	A0A1Y2HEJ3
E, I	Nucleotide cyclase	protein	182	35% helix, 36% strand	A0A1Y2HEJ3
K	Nucleotide cyclase	protein	183	35% helix, 34% strand	A0A1Y2HEJ3
M	Nucleotide cyclase	protein	180	36% helix, 35% strand	A0A1Y2HEJ3
N	Nucleotide cyclase	protein	181	36% helix, 36% strand	A0A1Y2HEJ3
O	Nucleotide cyclase	protein	179	36% helix, 36% strand	A0A1Y2HEJ3
P	Nucleotide cyclase	protein	179	36% helix, 35% strand	A0A1Y2HEJ3

Ligands and binding sites

T99 · Adenosine-5'-sp-alpha-thio-triphosphate · ligand · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
CA · Calcium ion · metal · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
GOL · Glycerol · additive · 15 copies · chains A, B, E, C, D, F, M, N, G, H, L, I, J, K, P, O

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	415	0.86	0.94	43	empty
2	394	0.85	0.93	51	empty
3	384	0.85	0.93	50	empty
4	346	0.85	0.94	43	empty
5	377	0.85	0.93	51	empty

Interfaces

31 interfaces between chains.

C–D · 1184 Å² buried · 6 hydrogen bonds · protein-protein
K–L · 1174 Å² buried · 7 hydrogen bonds · protein-protein
G–H · 1165 Å² buried · 7 hydrogen bonds · protein-protein
E–F · 1141 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 1137 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

5OYH · crystal structure of the catalytic core of a rhodopsin-guanylyl cyclase with converted… · 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 A0A1Y2HEJ3
Elsewhere: RCSB PDB 5OYH · PDBe 5OYH · UniProt A0A1Y2HEJ3

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