Research workbench

Wus-hd bound to taat DNA

Analyse Wus-hd bound to taat DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6RYL
Type: protein + DNA
Length: 380 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein wuschel; DNA (5'- D(P*CP*AP*CP*AP*AP*CP*CP*CP*AP*TP*TP*AP*AP*CP*AP*C)-3'); DNA…
UniProt: Q9SB92
Pockets: 12 · best druggability 0.75

Structure

x-ray diffraction · 5 distinct chains · 69% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein wuschel	protein	61	66% helix, 0% strand	Q9SB92
B, C, E	Protein wuschel	protein	64	70% helix, 0% strand	Q9SB92
D	Protein wuschel	protein	63	71% helix, 0% strand	Q9SB92
F, H	DNA (5'- D(PCPAPCPAPAPCPCPCPAPTPTPAPAPCPAPC)-3')	dna	16	—	—
G, I	DNA (5'- D(PGPTPGPTPTPAPAPTPGPGPGPTPTPGPTPG)-3')	dna	16	—	—

Pockets

12 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	803	0.75	0.80	70	empty
2	386	0.70	0.82	33	empty
3	256	0.61	0.80	26	empty
4	279	0.51	0.75	27	empty
5	88	0.42	0.79	14	empty

Interfaces

17 interfaces between chains.

H–I · 728 Å² buried · 81 hydrogen bonds · nucleic-nucleic
F–G · 716 Å² buried · 70 hydrogen bonds · nucleic-nucleic
C–F · 479 Å² buried · 10 hydrogen bonds · protein-nucleic
A–F · 464 Å² buried · 8 hydrogen bonds · protein-nucleic
E–H · 449 Å² buried · 7 hydrogen bonds · protein-nucleic

Compared structures

6RYL · WUS-HD bound to TAAT DNA · the same entry in another collection · chain I against I, TM-score 1.00
Q9SB92 · AlphaFold monomer V2.0 prediction for protein wuschel (Q9SB92) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q9SB92
Elsewhere: RCSB PDB 6RYL · PDBe 6RYL · UniProt Q9SB92

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