MolNFT v1 · #128610 · protein

PVHL:ELOB:ELOC in complex with (2S,4R)-1-((S)-2-(1- acetylcyclopropanecarboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4- (4-methylthiazol-5-YL)BENZYL)PYRROLIDINE-2-carboxamide (ligand 16)

5NVZ · Elongin-B: “PVHL:ELOB:ELOC in complex with (2S,4R)-1-((S)-2-(1- acetylcyclopropanecarboxamido)-3,3-dimethylbutanoyl)-4-hyd…”. X-ray diffraction, 1 ligand (9BN), 9 pockets (best druggability 0.62). MolNFT v1 #128610 on GenesisL1: 3D…

PDB: 5NVZ
Type: protein
Length: 1,339 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: 9BN
Pockets: 9 · best druggability 0.62

Structure

x-ray diffraction · 8 distinct chains · 32% helix, 26% 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	142	23% helix, 30% strand	P40337
D, G, J	Elongin-B	protein	103	15% helix, 37% strand	Q15370
E	Elongin-C	protein	91	46% helix, 14% strand	Q15369
F, I, L	Von hippel-lindau disease tumor suppressor	protein	143	25% helix, 31% strand	P40337
H	Elongin-C	protein	89	46% helix, 15% strand	Q15369
K	Elongin-C	protein	88	48% helix, 15% strand	Q15369

Ligands and binding sites

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

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	298	0.62	0.79	40	9BN
2	272	0.61	0.79	39	empty
3	150	0.42	0.75	23	empty
4	151	0.41	0.74	22	empty
5	126	0.37	0.73	23	empty

Interfaces

18 interfaces between chains.

G–H · 1140 Å² buried · 10 hydrogen bonds · protein-protein
J–K · 1135 Å² buried · 13 hydrogen bonds · protein-protein
D–E · 1128 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1122 Å² buried · 12 hydrogen bonds · protein-protein
E–F · 1054 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified (artifact).

Compared structures

5NVZ · pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-(1-acetylcyclopropanecarboxamido)-3,3-dime… · 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 5NVZ · PDBe 5NVZ · UniProt Q15370 · UniProt Q15369 · UniProt P40337

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