MolNFT v1 · #128613 · protein

PVHL:ELOB:ELOC in complex with (2S,4R)-1-((S)-3,3-dimethyl-2-(oxetane- 3-CARBOXAMIDO)BUTANOYL)-4-hydroxy-N-(4-(4-methylthiazol-5-YL)BENZYL) pyrrolidine-2-carboxamide (ligand 19)

5NW2 · Elongin-B: “PVHL:ELOB:ELOC in complex with (2S,4R)-1-((S)-3,3-dimethyl-2-(oxetane…”. X-ray diffraction, 1 ligand (9B8), 8 pockets (best druggability 0.65). MolNFT v1 #128613 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5NW2
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: 9B8
Pockets: 8 · best druggability 0.65

Structure

x-ray diffraction · 8 distinct chains · 32% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, J	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	26% helix, 30% strand	P40337
D, G	Elongin-B	protein	103	15% helix, 39% strand	Q15370
E	Elongin-C	protein	91	46% helix, 14% strand	Q15369
F, I, L	Von hippel-lindau disease tumor suppressor	protein	143	27% helix, 29% strand	P40337
H	Elongin-C	protein	89	46% helix, 15% strand	Q15369
K	Elongin-C	protein	88	44% helix, 15% strand	Q15369

Ligands and binding sites

9B8 · (2~{S},4~{R})-1-[(2~{S})-3,3-dimethyl-2-(oxetan-3-ylcarbonylamino)butanoyl]-~{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

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	276	0.65	0.81	39	9B8
2	293	0.62	0.79	43	9B8
3	174	0.49	0.77	30	empty
4	143	0.44	0.76	30	empty
5	146	0.44	0.76	27	empty

Interfaces

19 interfaces between chains.

G–H · 1144 Å² buried · 12 hydrogen bonds · protein-protein
J–K · 1138 Å² buried · 11 hydrogen bonds · protein-protein
D–E · 1129 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1122 Å² buried · 12 hydrogen bonds · protein-protein
E–F · 1070 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified (artifact).

Compared structures

5NW2 · pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-3,3-dimethyl-2-(oxetane-3-carboxamido)butano… · 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 5NW2 · PDBe 5NW2 · UniProt Q15370 · UniProt Q15369 · UniProt P40337

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