Research workbench

PVHL:ELOB:ELOC in complex with N-((S)-1-((2S,4R)-4-hydroxy-2-((4-(4- methylthiazol-5-YL)BENZYL)CARBAMOTHIOYL) pyrrolidin-1-yl)-1- oxopropan-2-YL)ACETAMIDE (ligand 2)

Analyse PVHL:ELOB:ELOC in complex with N-((S)-1-((2S,4R)-4-hydroxy-2-((4-(4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6FMI
Type: protein
Length: 660 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Elongin-B; Elongin-C; Von hippel-lindau disease tumor suppressor
UniProt: Q15370, Q15369, P40337
Ligands: DV2
Pockets: 7 · best druggability 0.50

Structure

x-ray diffraction · 3 distinct chains · 27% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Elongin-B	protein	103	15% helix, 39% strand	Q15370
B, E	Elongin-C	protein	86	45% helix, 15% strand	Q15369
C, F	Von hippel-lindau disease tumor suppressor	protein	141	24% helix, 30% strand	P40337

Ligands and binding sites

DV2 · ~{N}-[(2~{S})-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamothioyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-propan-2-yl]ethanamide · ligand · 2 copies · chains C, F

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	188	0.50	0.77	29	empty
2	135	0.42	0.75	22	empty
3	57	0.34	0.77	14	DV2
4	61	0.33	0.76	12	empty
5	57	0.30	0.75	12	empty

Interfaces

7 interfaces between chains.

A–B · 1170 Å² buried · 13 hydrogen bonds · protein-protein
D–E · 1142 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 1077 Å² buried · 12 hydrogen bonds · protein-protein
E–F · 1064 Å² buried · 15 hydrogen bonds · protein-protein
C–F · 321 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 modified (artifact).

Compared structures

6FMI · pVHL:EloB:EloC in complex with N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4-methylthiazol-5-yl)ben… · the same entry in another collection · chain D against D, 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 C against A, TM-score 0.99
Q15369 · AlphaFold monomer V2.0 prediction for elongin-C (Q15369) · a predicted model of the same protein · chain B against A, TM-score 0.98
Q15370 · AlphaFold monomer V2.0 prediction for elongin-B (Q15370) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 6FMI · PDBe 6FMI · UniProt Q15370 · UniProt Q15369 · UniProt P40337

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