Research workbench

PVHL:ELOB:ELOC in complex with (2S,4R)-1-((S)-2-acetamidopropanoyl)-4- hydroxy-N-(4-(4-methylthiazol-5-YL)BENZYL) pyrrolidine-2-carboxamide (ligand 11)

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

PDB: 5NVY
Type: protein
Length: 1,338 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: 9B5
Pockets: 9 · best druggability 0.58

Structure

x-ray diffraction · 8 distinct chains · 32% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Elongin-B	protein	104	17% helix, 38% strand	Q15370
B	Elongin-C	protein	87	48% helix, 15% strand	Q15369
C	Von hippel-lindau disease tumor suppressor	protein	141	22% helix, 30% strand	P40337
D, G, J	Elongin-B	protein	103	15% helix, 35% strand	Q15370
E	Elongin-C	protein	91	46% helix, 14% strand	Q15369
F, I, L	Von hippel-lindau disease tumor suppressor	protein	143	26% helix, 30% strand	P40337
H	Elongin-C	protein	89	48% helix, 15% strand	Q15369
K	Elongin-C	protein	88	48% helix, 15% strand	Q15369

Ligands and binding sites

9B5 · (2~{S},4~{R})-1-[(2~{S})-2-acetamidopropanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide · ligand · 4 copies · chains C, L, F, I

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

Pockets

9 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	225	0.58	0.79	34	9B5
2	252	0.55	0.77	33	9B5
3	148	0.42	0.75	28	empty
4	137	0.41	0.75	20	empty
5	154	0.40	0.74	23	empty

Interfaces

19 interfaces between chains.

D–E · 1157 Å² buried · 14 hydrogen bonds · protein-protein
G–H · 1154 Å² buried · 15 hydrogen bonds · protein-protein
J–K · 1150 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1137 Å² buried · 13 hydrogen bonds · protein-protein
E–F · 1088 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified (artifact).

Compared structures

5NVY · pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-acetamidopropanoyl)-4-hydroxy-N-(4-(4-meth… · 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 5NVY · PDBe 5NVY · UniProt Q15370 · UniProt Q15369 · UniProt P40337

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