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Crystal structure of nova-2 KH3 K-homology RNA-binding domain

Analyse Crystal structure of nova-2 KH3 K-homology RNA-binding domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1DTJ
Type: protein
Length: 266 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA-binding neurooncological ventral antigen 2
UniProt: Q9UNW9
Pockets: 3 · best druggability 0.47

Structure

x-ray diffraction · 4 distinct chains · 47% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA-binding neurooncological ventral antigen 2	protein	74	39% helix, 27% strand	Q9UNW9
B	RNA-binding neurooncological ventral antigen 2	protein	62	44% helix, 32% strand	Q9UNW9
C	RNA-binding neurooncological ventral antigen 2	protein	66	52% helix, 30% strand	Q9UNW9
D	RNA-binding neurooncological ventral antigen 2	protein	64	55% helix, 31% strand	Q9UNW9

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	177	0.47	0.75	27	empty
2	86	0.45	0.80	27	empty
3	52	0.30	0.76	11	empty

Interfaces

6 interfaces between chains.

B–C · 558 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 491 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 463 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 433 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 44 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

1DTJ · Crystal structure of nova-2 KH3 K-homology RNA-binding domain · the same entry in another collection · chain D against D, TM-score 1.00
Q9UNW9 · AlphaFold monomer V2.0 prediction for RNA-binding protein nova-2 (Q9UNW9) · a predicted model of the same protein · chain D against A, TM-score 0.96

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 Q9UNW9
Elsewhere: RCSB PDB 1DTJ · PDBe 1DTJ · UniProt Q9UNW9

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