MolNFT v1 · #161197 · protein + DNA

Recognition of different base tetrads by rhau: X-ray crystal structure of G4 recognition motif bound to the 3-end tetrad of a DNA G- quadruplex

6Q6R · Parallel stranded DNA G-quadruplex: “Recognition of different base tetrads by rhau: X-ray crystal structure of G4 recognition motif bound to the…”. X-ray diffraction, 1 ligand (K), 5 pockets (best druggability 0.52). MolNFT v1…

PDB: 6Q6R
Type: protein + DNA
Length: 132 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Parallel stranded DNA G-quadruplex; ATP-dependent DNA/RNA helicase DHX36
EC: 3.6.4.12, 3.6.4.13
UniProt: Q9H2U1
Ligands: K
Pockets: 5 · best druggability 0.52

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Parallel stranded DNA G-quadruplex	dna	16	—	—
E, F, G, H	ATP-dependent DNA/RNA helicase DHX36 (EC 3.6.4.12, 3.6.4.13)	protein	17	47% helix, 0% strand	Q9H2U1

Ligands and binding sites

K · Potassium ion · metal · 10 copies · chains A, E, B, F, C, G, D, H

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	277	0.52	0.76	21	empty
2	90	0.36	0.76	12	empty
3	75	0.33	0.76	14	empty
4	62	0.30	0.76	12	empty
5	68	0.30	0.75	13	empty

Interfaces

8 interfaces between chains.

C–D · 482 Å² buried · 20 hydrogen bonds · nucleic-nucleic
A–B · 482 Å² buried · 18 hydrogen bonds · nucleic-nucleic
B–F · 404 Å² buried · 3 hydrogen bonds · protein-nucleic
A–E · 398 Å² buried · 2 hydrogen bonds · protein-nucleic
C–G · 384 Å² buried · 4 hydrogen bonds · protein-nucleic

Compared structures

6Q6R · Recognition of different base tetrads by RHAU: X-ray crystal structure of G4 recognition… · the same entry in another collection · chain H against H, TM-score 1.00
Q9H2U1 · AlphaFold monomer V2.0 prediction for ATP-dependent DNA/RNA helicase DHX36 (Q9H2U1) · a predicted model of the same protein · chain F against A, TM-score 0.60

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 Q9H2U1
Elsewhere: RCSB PDB 6Q6R · PDBe 6Q6R · UniProt Q9H2U1

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