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WDR5 in complex with unmodified H3K4 peptide

Analyse WDR5 in complex with unmodified H3K4 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2H9M
Type: protein
Length: 619 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Wd-repeat protein 5; H3 histone
UniProt: P61964, Q6P823
Pockets: 3 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 0% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Wd-repeat protein 5	protein	304	0% helix, 50% strand	P61964
B	H3 histone	protein	6	0% helix, 0% strand	Q6P823
D	H3 histone	protein	5	0% helix, 0% strand	Q6P823

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	486	0.73	0.82	45	empty
2	488	0.72	0.81	44	empty
3	411	0.62	0.77	49	empty

Interfaces

4 interfaces between chains.

A–B · 498 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 459 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 136 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 69 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

2H9M · WDR5 in complex with unmodified H3K4 peptide · the same entry in another collection · chain C against C, TM-score 1.00
Q6P823 · AlphaFold monomer V2.0 prediction for histone H3.3 (Q6P823) · a predicted model of the same protein · chain D against A, TM-score 0.70

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 P61964
Every structure of UniProt Q6P823
Elsewhere: RCSB PDB 2H9M · PDBe 2H9M · UniProt P61964 · UniProt Q6P823

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