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PVHL54-213-elob-eloc complex _ (2S,4R)-N-((1,1'-biphenyl)-4-ylmethyl)- 4-hydroxy-1-(2-(3-methylisoxazol-5-YL)ACETYL)PYRROLIDINE-2- carboxamide

Analyse PVHL54-213-elob-eloc complex _ (2S,4R)-N-((1,1'-biphenyl)-4-ylmethyl)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3ZTC
Type: protein
Length: 1,328 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transcription elongation factor B polypeptide 2; Transcription elongation factor B…
UniProt: Q15370, Q15369, P40337
Ligands: TR0
Pockets: 11 · best druggability 0.63

Structure

x-ray diffraction · 11 distinct chains · 27% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transcription elongation factor B polypeptide 2	protein	103	18% helix, 35% strand	Q15370
B	Transcription elongation factor B polypeptide 1	protein	86	48% helix, 15% strand	Q15369
C	Von hippel-lindau disease tumor suppressor	protein	141	23% helix, 30% strand	P40337
D	Transcription elongation factor B polypeptide 2	protein	99	15% helix, 35% strand	Q15370
E, K	Transcription elongation factor B polypeptide 1	protein	87	48% helix, 15% strand	Q15369
F	Von hippel-lindau disease tumor suppressor	protein	142	23% helix, 28% strand	P40337
G	Transcription elongation factor B polypeptide 2	protein	105	24% helix, 36% strand	Q15370
H	Transcription elongation factor B polypeptide 1	protein	86	48% helix, 15% strand	Q15369
I	Von hippel-lindau disease tumor suppressor	protein	145	26% helix, 29% strand	P40337
J	Transcription elongation factor B polypeptide 2	protein	104	18% helix, 31% strand	Q15370
L	Von hippel-lindau disease tumor suppressor	protein	143	24% helix, 29% strand	P40337

Ligands and binding sites

TR0 · (4R)-N-(biphenyl-4-ylmethyl)-4-hydroxy-1-[(3-methylisoxazol-5-yl)acetyl]-L-prolinamide · ligand · 4 copies · chains C, F, I, L

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

Pockets

11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	348	0.63	0.79	44	TR0
2	296	0.62	0.79	35	TR0
3	120	0.55	0.82	23	empty
4	184	0.46	0.75	36	empty
5	76	0.45	0.81	17	empty

Interfaces

17 interfaces between chains.

G–H · 1118 Å² buried · 16 hydrogen bonds · protein-protein
J–K · 1114 Å² buried · 10 hydrogen bonds · protein-protein
D–E · 1079 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1066 Å² buried · 13 hydrogen bonds · protein-protein
E–F · 1059 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

3ZTC · pVHL54-213-EloB-EloC complex _ (2S,4R)-N-((1,1'-biphenyl)-4-ylmethyl)… · 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 3ZTC · PDBe 3ZTC · UniProt Q15370 · UniProt Q15369 · UniProt P40337

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