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Structure of the human nuclear cap-binding-complex (cbc) in complex with a cap analogue M7GPPPG

Analyse Structure of the human nuclear cap-binding-complex (cbc) in complex with a cap… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1H2U
Type: protein
Length: 1,708 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 80 kda nuclear cap binding protein; 20 kda nuclear cap binding protein
UniProt: Q09161, P52298
Ligands: GDP, 7MG
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 61% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	80 kda nuclear cap binding protein	protein	706	67% helix, 1% strand	Q09161
B	80 kda nuclear cap binding protein	protein	706	68% helix, 1% strand	Q09161
X	20 kda nuclear cap binding protein	protein	149	29% helix, 22% strand	P52298
Y	20 kda nuclear cap binding protein	protein	147	29% helix, 24% strand	P52298

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains X, Y
7MG · 7N-methyl-8-hydroguanosine-5'-monophosphate · ligand · 2 copies · chains X, Y

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

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	747	0.79	0.83	54	empty
2	734	0.79	0.83	59	empty
3	543	0.75	0.82	54	empty
4	595	0.74	0.81	64	empty
5	439	0.69	0.80	68	empty

Interfaces

4 interfaces between chains.

A–X · 1754 Å² buried · 26 hydrogen bonds · protein-protein
B–Y · 1707 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 403 Å² buried · 3 hydrogen bonds · protein-protein
B–X · 131 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

1H2U · Structure of the human nuclear cap-binding-complex (CBC) in complex with a cap analogue… · the same entry in another collection · chain Y against Y, TM-score 1.00
Q09161 · AlphaFold monomer V2.0 prediction for nuclear cap-binding protein subunit 1 (Q09161) · a predicted model of the same protein · chain B against A, TM-score 1.00
P52298 · AlphaFold monomer V2.0 prediction for nuclear cap-binding protein subunit 2 (P52298) · a predicted model of the same protein · chain Y 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 Q09161
Every structure of UniProt P52298
Elsewhere: RCSB PDB 1H2U · PDBe 1H2U · UniProt Q09161 · UniProt P52298

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