Research workbench

PVHL:ELOB:ELOC in complex with methyl 4H-FURO[3,2-B]PYRROLE-5- carboxylate

Analyse PVHL:ELOB:ELOC in complex with methyl 4H-FURO[3,2-B]PYRROLE-5- carboxylate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6GMN
Type: protein
Length: 1,324 residues
Chains: 12
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: F4E
Pockets: 8 · best druggability 0.59

Structure

x-ray diffraction · 9 distinct chains · 29% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G, J	Elongin-B	protein	103	15% helix, 37% strand	Q15370
B, E	Elongin-C	protein	87	48% helix, 15% strand	Q15369
C	Von hippel-lindau disease tumor suppressor	protein	137	23% helix, 31% strand	P40337
D	Elongin-B	protein	100	15% helix, 36% strand	Q15370
F	Von hippel-lindau disease tumor suppressor	protein	142	27% helix, 30% strand	P40337
H	Elongin-C	protein	86	49% helix, 15% strand	Q15369
I	Von hippel-lindau disease tumor suppressor	protein	145	26% helix, 29% strand	P40337
K	Elongin-C	protein	87	47% helix, 15% strand	Q15369
L	Von hippel-lindau disease tumor suppressor	protein	144	25% helix, 29% strand	P40337

Ligands and binding sites

F4E · methyl 4~{H}-furo[3,2-b]pyrrole-5-carboxylate · ligand · 2 copies · chains B, K
ACT · Acetate ion · additive · 5 copies · chains A, B, C, E, F, H, I, K, L

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

Pockets

8 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	241	0.59	0.79	34	empty
2	248	0.59	0.79	38	F4E
3	163	0.42	0.74	24	empty
4	135	0.41	0.75	24	empty
5	124	0.38	0.74	24	empty

Interfaces

15 interfaces between chains.

J–K · 1144 Å² buried · 14 hydrogen bonds · protein-protein
G–H · 1138 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1124 Å² buried · 12 hydrogen bonds · protein-protein
D–E · 1100 Å² buried · 13 hydrogen bonds · protein-protein
E–F · 1086 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 modified (artifact).

Compared structures

6GMN · pVHL:EloB:EloC in complex with methyl 4H-furo[3,2-b]pyrrole-5-carboxylate · the same entry in another collection · chain L against L, 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 Q15370
Every structure of UniProt Q15369
Every structure of UniProt P40337
Elsewhere: RCSB PDB 6GMN · PDBe 6GMN · UniProt Q15370 · UniProt Q15369 · UniProt P40337

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