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Complex of human nuclear cap-binding complex with M7GTP and nelf-E C-terminal peptide

Analyse Complex of human nuclear cap-binding complex with M7GTP and nelf-E C-terminal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5OOB
Type: protein
Length: 3,566 residues
Chains: 11
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.79
Source: Homo sapiens; SYNTHETIC CONSTRUCT
Molecule: Nuclear cap-binding protein subunit 1; Nuclear cap-binding protein subunit 2; Negative…
UniProt: Q09161, P52298, P18615
Ligands: MGT
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · resolution 2.79 · 11 distinct chains · 62% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nuclear cap-binding protein subunit 1	protein	739	70% helix, 1% strand	Q09161
B	Nuclear cap-binding protein subunit 2	protein	152	31% helix, 20% strand	P52298
C	Nuclear cap-binding protein subunit 1	protein	731	70% helix, 1% strand	Q09161
D	Nuclear cap-binding protein subunit 2	protein	151	28% helix, 19% strand	P52298
E	Negative elongation factor E	protein	18	0% helix, 0% strand	P18615
F	Nuclear cap-binding protein subunit 1	protein	718	71% helix, 1% strand	Q09161
G	Nuclear cap-binding protein subunit 2	protein	149	29% helix, 19% strand	P52298
I	Nuclear cap-binding protein subunit 1	protein	729	70% helix, 1% strand	Q09161
J	Nuclear cap-binding protein subunit 2	protein	148	29% helix, 20% strand	P52298
K	Negative elongation factor E	protein	17	0% helix, 0% strand	P18615
Z	Negative elongation factor E	protein	14	0% helix, 7% strand	P18615

Ligands and binding sites

MGT · 7N-methyl-8-hydroguanosine-5'-triphosphate · ligand · 4 copies · chains B, D, G, J

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	747	0.79	0.83	52	empty
2	705	0.79	0.84	50	empty
3	710	0.79	0.83	50	empty
4	735	0.78	0.82	56	empty
5	557	0.76	0.83	63	empty

Interfaces

18 interfaces between chains.

C–D · 1830 Å² buried · 32 hydrogen bonds · protein-protein
I–J · 1808 Å² buried · 29 hydrogen bonds · protein-protein
F–G · 1805 Å² buried · 30 hydrogen bonds · protein-protein
A–B · 1799 Å² buried · 27 hydrogen bonds · protein-protein
C–E · 721 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5OOB · Complex of human nuclear cap-binding complex with M7GTP and nelf-E C- terminal peptide · the same entry in another collection · chain Z against Z, 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 F 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 Q09161
Every structure of UniProt P52298
Every structure of UniProt P18615
Elsewhere: RCSB PDB 5OOB · PDBe 5OOB · UniProt Q09161 · UniProt P52298 · UniProt P18615

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