MolNFT v1 · #63870 · protein

Crystal structure of the nucleoporin NUP214 in complex with the dead- box helicase DDX19

3FMO · Nuclear pore complex protein NUP214: “Crystal structure of the nucleoporin NUP214 in complex with the dead- box helicase DDX19”. X-ray diffraction, 1 ligand (ADP), 13 pockets (best druggability 0.78). MolNFT v1 #63870 on GenesisL1…

PDB: 3FMO
Type: protein
Length: 653 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nuclear pore complex protein NUP214; ATP-dependent RNA helicase DDX19B
EC: 3.6.1.-
UniProt: P35658, Q9UMR2
Ligands: ADP
Pockets: 13 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 16% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nuclear pore complex protein NUP214	protein	421	4% helix, 44% strand	P35658
B	ATP-dependent RNA helicase DDX19B (EC 3.6.1.-)	protein	232	36% helix, 15% strand	Q9UMR2

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · chains B
GOL · Glycerol · additive · chains A

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

Pockets

13 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	788	0.78	0.81	53	empty
2	583	0.76	0.83	77	empty
3	87	0.54	0.85	17	empty
4	170	0.50	0.78	23	empty
5	143	0.49	0.78	23	empty

Interfaces

1 interface between chains.

A–B · 1120 Å² buried · 31 hydrogen bonds · protein-protein

Compared structures

3FMO · Crystal structure of the nucleoporin Nup214 in complex with the DEAD-box helicase Ddx19 · the same entry in another collection · chain A against A, TM-score 1.00
P35658 · AlphaFold monomer V2.0 prediction for nuclear pore complex protein NUP214 (P35658) · a predicted model of the same protein · chain A against A, TM-score 0.99
Q9UMR2 · AlphaFold monomer V2.0 prediction for ATP-dependent RNA helicase DDX19B (Q9UMR2) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 P35658
Every structure of UniProt Q9UMR2
Elsewhere: RCSB PDB 3FMO · PDBe 3FMO · UniProt P35658 · UniProt Q9UMR2

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