MolNFT v1 · #183610 · protein

Co-crystal structure of UPF3B-rrm-nops-L with UPF2-MIF4GIII

7NWU · Regulator of nonsense transcripts 3B: “Co-crystal structure of UPF3B-rrm-nops-L with UPF2-MIF4GIII”. X-ray diffraction, 20 pockets (best druggability 0.82). MolNFT v1 #183610 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 7NWU
Type: protein
Length: 1,466 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Regulator of nonsense transcripts 3B; Regulator of nonsense transcripts 2
UniProt: Q9BZI7, Q9HAU5
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 6 distinct chains · 48% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Regulator of nonsense transcripts 3B	protein	122	25% helix, 26% strand	Q9BZI7
B, F	Regulator of nonsense transcripts 2	protein	250	70% helix, 0% strand	Q9HAU5
C	Regulator of nonsense transcripts 3B	protein	115	25% helix, 28% strand	Q9BZI7
D, H	Regulator of nonsense transcripts 2	protein	250	69% helix, 0% strand	Q9HAU5
E	Regulator of nonsense transcripts 3B	protein	114	25% helix, 28% strand	Q9BZI7
G	Regulator of nonsense transcripts 3B	protein	115	25% helix, 28% strand	Q9BZI7

Ligands and binding sites

1PE · Pentaethylene glycol · additive · 2 copies · chains D, H
PG4 · Tetraethylene glycol · additive · chains F

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

Pockets

20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	847	0.82	0.84	95	empty
2	731	0.81	0.84	83	empty
3	425	0.59	0.75	46	empty
4	356	0.57	0.75	38	empty
5	55	0.48	0.85	15	empty

Interfaces

16 interfaces between chains.

A–B · 1895 Å² buried · 30 hydrogen bonds · protein-protein
E–F · 1839 Å² buried · 30 hydrogen bonds · protein-protein
G–H · 1740 Å² buried · 27 hydrogen bonds · protein-protein
C–D · 1721 Å² buried · 25 hydrogen bonds · protein-protein
F–H · 847 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

7NWU · Co-crystal structure of UPF3B-RRM-NOPS-L with UPF2-MIF4GIII · the same entry in another collection · chain H against H, TM-score 1.00
Q9HAU5 · AlphaFold monomer V2.0 prediction for regulator of nonsense transcripts 2 (Q9HAU5) · a predicted model of the same protein · chain B against A, TM-score 0.99
Q9BZI7 · AlphaFold monomer V2.0 prediction for regulator of nonsense transcripts 3B (Q9BZI7) · a predicted model of the same protein · chain C against A, TM-score 0.80

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 Q9BZI7
Every structure of UniProt Q9HAU5
Elsewhere: RCSB PDB 7NWU · PDBe 7NWU · UniProt Q9BZI7 · UniProt Q9HAU5

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