MolNFT v1 · #149973 · protein

PVHL:ELOB:ELOC in complex with modified hif-1A codd peptide containing (3R,4S)-3-fluoro-4-hydroxyproline (ligand 13A)

6GFX · Elongin-B: “PVHL:ELOB:ELOC in complex with modified hif-1A codd peptide containing (3R,4S)-3-fluoro-4-hydroxyproline…”. X-ray diffraction, 1 pocket (best druggability 0.42). MolNFT v1 #149973 on GenesisL1: 3D structure, binding…

PDB: 6GFX
Type: protein
Length: 355 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; Fluorinated…
UniProt: Q15370, Q15369, P40337
Pockets: 1 · best druggability 0.42

Structure

x-ray diffraction · 4 distinct chains · 29% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Elongin-B	protein	104	20% helix, 35% strand	Q15370
B	Elongin-C	protein	88	48% helix, 15% strand	Q15369
C	Von hippel-lindau disease tumor suppressor	protein	147	28% helix, 29% strand	P40337
D	Fluorinated hypoxia-inducible factor 1 alpha peptide	protein	16	0% helix, 19% strand	—

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	171	0.42	0.73	23	empty

Interfaces

5 interfaces between chains.

A–B · 1188 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 1091 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 957 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 203 Å² buried · 1 hydrogen bond · protein-protein
B–D · 48 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 modified (nonstandard).

Compared structures

6GFX · pVHL:EloB:EloC in complex with modified HIF-1a CODD peptide containing… · the same entry in another collection · chain A against A, TM-score 1.00
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
Q15369 · AlphaFold monomer V2.0 prediction for elongin-C (Q15369) · a predicted model of the same protein · chain B 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 6GFX · PDBe 6GFX · UniProt Q15370 · UniProt Q15369 · UniProt P40337

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