MolNFT v1 · #185811 · protein

Co-crystal structure of UPF3A-rrm-nops-L with UPF2-MIF4GIII

7QG6 · Regulator of nonsense transcripts 3A: “Co-crystal structure of UPF3A-rrm-nops-L with UPF2-MIF4GIII”. X-ray diffraction, 1 ligand (CL), 16 pockets (best druggability 0.82). MolNFT v1 #185811 on GenesisL1: 3D structure, binding sites…

PDB: 7QG6
Type: protein
Length: 1,458 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Regulator of nonsense transcripts 3A; Regulator of nonsense transcripts 2
UniProt: Q9H1J1, Q9HAU5
Ligands: CL
Pockets: 16 · best druggability 0.82

Structure

x-ray diffraction · 8 distinct chains · 54% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Regulator of nonsense transcripts 3A	protein	117	24% helix, 26% strand	Q9H1J1
D	Regulator of nonsense transcripts 2	protein	245	70% helix, 0% strand	Q9HAU5
A	Regulator of nonsense transcripts 3A	protein	123	22% helix, 25% strand	Q9H1J1
B	Regulator of nonsense transcripts 2	protein	248	70% helix, 0% strand	Q9HAU5
E	Regulator of nonsense transcripts 3A	protein	119	25% helix, 24% strand	Q9H1J1
F	Regulator of nonsense transcripts 2	protein	246	69% helix, 0% strand	Q9HAU5
G	Regulator of nonsense transcripts 3A	protein	116	20% helix, 27% strand	Q9H1J1
H	Regulator of nonsense transcripts 2	protein	244	70% helix, 1% strand	Q9HAU5

Ligands and binding sites

CL · Chloride ion · ion · chains F
PGE · Triethylene glycol · additive · 3 copies · chains D, B, F

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

Pockets

16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	991	0.82	0.83	116	empty
2	232	0.77	0.91	35	empty
3	144	0.70	0.90	21	empty
4	219	0.67	0.85	31	empty
5	168	0.64	0.85	29	empty

Interfaces

10 interfaces between chains.

A–B · 1794 Å² buried · 21 hydrogen bonds · protein-protein
E–F · 1663 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 1634 Å² buried · 28 hydrogen bonds · protein-protein
G–H · 1618 Å² buried · 23 hydrogen bonds · protein-protein
D–B · 747 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7QG6 · Co-crystal structure of UPF3A-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 F against A, TM-score 0.99

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 Q9H1J1
Every structure of UniProt Q9HAU5
Elsewhere: RCSB PDB 7QG6 · PDBe 7QG6 · UniProt Q9H1J1 · UniProt Q9HAU5

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