MolNFT v1 · #174532 · protein

The crystal structure of mouse ORF10-RAE1-NUP98 complex

7BYF · MRNA export factor: “The crystal structure of mouse ORF10-RAE1-NUP98 complex”. X-ray diffraction, 2 ligands (HG, NA), 18 pockets (best druggability 0.82). MolNFT v1 #174532 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 7BYF
Type: protein
Length: 1,577 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MRNA export factor; Peptidase S59 domain-containing protein; 10 protein
UniProt: Q8C570, Q3TPG3, O41931
Ligands: HG, NA
Pockets: 18 · best druggability 0.82

Structure

x-ray diffraction · 6 distinct chains · 5% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MRNA export factor	protein	337	2% helix, 51% strand	Q8C570
B	Peptidase S59 domain-containing protein	protein	52	25% helix, 21% strand	Q3TPG3
F	10 protein	protein	393	5% helix, 47% strand	O41931
C	10 protein	protein	399	3% helix, 46% strand	O41931
D	MRNA export factor	protein	339	3% helix, 49% strand	Q8C570
E	Peptidase S59 domain-containing protein	protein	57	23% helix, 26% strand	Q3TPG3

Ligands and binding sites

HG · Mercury (II) ion · metal · 24 copies · chains A, F, C, D
NA · Sodium ion · metal · 4 copies · chains F, C, D

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

Pockets

18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	853	0.82	0.84	68	HG
2	902	0.82	0.84	70	HG
3	674	0.80	0.85	86	NA, HG
4	509	0.72	0.81	62	HG
5	296	0.67	0.82	29	HG

Interfaces

9 interfaces between chains.

A–B · 1517 Å² buried · 31 hydrogen bonds · protein-protein
D–E · 1483 Å² buried · 30 hydrogen bonds · protein-protein
F–D · 1344 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 1273 Å² buried · 20 hydrogen bonds · protein-protein
A–F · 591 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7BYF · The crystal structure of mouse ORF10-Rae1-Nup98 complex · the same entry in another collection · chain E against E, TM-score 1.00
Q8C570 · AlphaFold monomer V2.0 prediction for mRNA export factor (Q8C570) · a predicted model of the same protein · 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 Q8C570
Every structure of UniProt Q3TPG3
Every structure of UniProt O41931
Elsewhere: RCSB PDB 7BYF · PDBe 7BYF · UniProt Q8C570 · UniProt Q3TPG3 · UniProt O41931

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