MolNFT v1 · #46611 · protein

WDR5 in complex with dimethylated H3K4 peptide

2O9K · Wd repeat protein 5: “WDR5 in complex with dimethylated H3K4 peptide”. X-ray diffraction, 4 pockets (best druggability 0.84). MolNFT v1 #46611 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2O9K
Type: protein
Length: 618 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Wd repeat protein 5; H3 histone
UniProt: P61964
Pockets: 4 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 0% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Wd repeat protein 5	protein	304	0% helix, 51% strand	P61964
B	H3 histone	protein	6	0% helix, 0% strand	—
C	Wd repeat protein 5	protein	303	0% helix, 51% strand	P61964
D	H3 histone	protein	5	0% helix, 0% strand	—

Pockets

4 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	896	0.84	0.86	69	empty
2	471	0.74	0.83	44	empty
3	142	0.56	0.82	26	empty
4	62	0.56	0.88	17	empty

Interfaces

3 interfaces between chains.

A–B · 572 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 524 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 496 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (methylation).

Compared structures

2O9K · WDR5 in Complex with Dimethylated H3K4 Peptide · the same entry in another collection · chain B against B, TM-score 1.00

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
Elsewhere: RCSB PDB 2O9K · PDBe 2O9K · UniProt P61964

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