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Quaternary complex of human WDR5 and PVHL:ELONGINC:ELONGINB bound to protac homer

Analyse Quaternary complex of human WDR5 and PVHL:ELONGINC:ELONGINB bound to protac… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7Q2J
Type: protein
Length: 642 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Elongin-B; Elongin-C; Von hippel-lindau disease tumor suppressor; Wd repeat-containing…
UniProt: Q15370, Q15369, P40337, P61964
Ligands: 8KH
Pockets: 5 · best druggability 0.70

Structure

x-ray diffraction · 4 distinct chains · 15% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Elongin-B	protein	103	15% helix, 37% strand	Q15370
B	Elongin-C	protein	88	49% helix, 15% strand	Q15369
C	Von hippel-lindau disease tumor suppressor	protein	147	24% helix, 30% strand	P40337
D	Wd repeat-containing protein 5	protein	304	0% helix, 51% strand	P61964

Ligands and binding sites

8KH · N-[5-[4-[[5-[[(2S)-3,3-dimethyl-1-[(2S,4R)-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]amino]-5-oxidanylidene-pentyl]carbamoyl]phenyl]-2-(4-methylpiperazin-1-yl)phenyl]-6-oxidanylidene-4-(trifluoromethyl)-1H-pyridine-3-carboxamide · ligand · chains C, D

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	450	0.70	0.81	33	empty
2	550	0.68	0.78	55	8KH
3	157	0.47	0.77	29	empty
4	55	0.47	0.85	16	empty
5	65	0.34	0.76	14	empty

Interfaces

4 interfaces between chains.

A–B · 1134 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 1089 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 212 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 141 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7Q2J · Quaternary Complex of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC Homer · the same entry in another collection · chain A against A, TM-score 1.00
Q15369 · AlphaFold monomer V2.0 prediction for elongin-C (Q15369) · a predicted model of the same protein · chain B against A, TM-score 0.97
Q15370 · AlphaFold monomer V2.0 prediction for elongin-B (Q15370) · 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 Q15370
Every structure of UniProt Q15369
Every structure of UniProt P40337
Every structure of UniProt P61964
Elsewhere: RCSB PDB 7Q2J · PDBe 7Q2J · UniProt Q15370 · UniProt Q15369 · UniProt P40337 · UniProt P61964

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