Research workbench

pVHL:EloB:EloC in complex with (4-(1H-pyrrol-1-yl)phenyl)methanol

Analyse pVHL:EloB:EloC in complex with (4-(1H-pyrrol-1-yl)phenyl)methanol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6GMR
Type: protein
Length: 359 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.75
Source: Homo sapiens; SYNTHETIC CONSTRUCT
Molecule: Elongin-B; Elongin-C; Hypoxia inducible factor 1alpha, residues 559-577; von…
UniProt: Q15370, Q15369, P40337
Ligands: F4K, SO4
Pockets: 1 · best druggability 0.54

Structure

x-ray diffraction · resolution 1.75 · 4 distinct chains · 28% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Elongin-B	protein	105	20% helix, 38% strand	Q15370
C	Elongin-C	protein	89	46% helix, 15% strand	Q15369
H	Hypoxia inducible factor 1alpha, residues 559-577	protein	16	0% helix, 19% strand	—
V	von Hippel-Lindau disease tumor suppressor	protein	149	26% helix, 30% strand	P40337

Ligands and binding sites

F4K · (4-pyrrol-1-ylphenyl)methanol · ligand · chains V
SO4 · Sulfate ion · ion · chains B, C
GOL · Glycerol · additive · chains C, V

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	253	0.54	0.76	32	F4K

Interfaces

4 interfaces between chains.

B–C · 1169 Å² buried · 13 hydrogen bonds · protein-protein
C–V · 1086 Å² buried · 12 hydrogen bonds · protein-protein
H–V · 900 Å² buried · 19 hydrogen bonds · protein-protein
B–V · 198 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 1 modified (hydroxylation).

Compared structures

6GMR · PVHL:ELOB:ELOC in complex with (4-(1H-pyrrol-1-YL)PHENYL)METHANOL · the same entry in another collection · chain B against B, TM-score 1.00
P40337 · AlphaFold monomer V2.0 prediction for von hippel-lindau disease tumor suppressor (P40337) · a predicted model of the same protein · chain V against A, TM-score 0.99
Q15370 · AlphaFold monomer V2.0 prediction for elongin-B (Q15370) · a predicted model of the same protein · chain B against A, TM-score 0.99
Q15369 · AlphaFold monomer V2.0 prediction for elongin-C (Q15369) · a predicted model of the same protein · chain C against A, TM-score 0.95

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
Elsewhere: RCSB PDB 6GMR · PDBe 6GMR · UniProt Q15370 · UniProt Q15369 · UniProt P40337

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