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Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide

Analyse Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5OO6
Type: protein
Length: 7,137 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nuclear cap-binding protein subunit 1; Nuclear cap-binding protein subunit 2; Serrate RNA…
UniProt: Q09161, P52298, Q9BXP5
Ligands: MGT
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 7 distinct chains · 66% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, S, V	Nuclear cap-binding protein subunit 1	protein	726	70% helix, 1% strand	Q09161
B, E, H, K, N, Q, T, W	Nuclear cap-binding protein subunit 2	protein	148	27% helix, 22% strand	P52298
D, M	Nuclear cap-binding protein subunit 1	protein	740	69% helix, 1% strand	Q09161
G, J, P	Nuclear cap-binding protein subunit 1	protein	730	70% helix, 1% strand	Q09161
C, F, O, R, X	Serrate RNA effector molecule homolog	protein	14	0% helix, 7% strand	Q9BXP5
I	Serrate RNA effector molecule homolog	protein	13	0% helix, 8% strand	Q9BXP5
L, U	Serrate RNA effector molecule homolog	protein	11	0% helix, 9% strand	Q9BXP5

Ligands and binding sites

MGT · 7N-methyl-8-hydroguanosine-5'-triphosphate · ligand · 8 copies · chains B, E, H, K, N, Q, T, W

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	888	0.80	0.83	81	empty
2	821	0.80	0.83	92	empty
3	885	0.80	0.82	103	empty
4	867	0.79	0.82	59	empty
5	781	0.78	0.82	54	empty

Interfaces

43 interfaces between chains.

S–T · 1856 Å² buried · 30 hydrogen bonds · protein-protein
P–Q · 1855 Å² buried · 33 hydrogen bonds · protein-protein
G–H · 1854 Å² buried · 33 hydrogen bonds · protein-protein
D–E · 1852 Å² buried · 38 hydrogen bonds · protein-protein
J–K · 1852 Å² buried · 31 hydrogen bonds · protein-protein

Compared structures

5OO6 · Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide · the same entry in another collection · chain P against P, 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 Q09161
Every structure of UniProt P52298
Every structure of UniProt Q9BXP5
Elsewhere: RCSB PDB 5OO6 · PDBe 5OO6 · UniProt Q09161 · UniProt P52298 · UniProt Q9BXP5

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