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pVHL54-213-EloB-EloC complex _ methyl 4-(((2S,4R)-4-hydroxy-1-(2-(3- methylisoxazol-5-yl)acetyl)pyrrolidine-2-carboxamido)methyl)benzoate

Analyse pVHL54-213-EloB-EloC complex _ methyl 4-(((2S,4R)-4-hydroxy-1-(2-(3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3ZTD
Type: protein
Length: 1,320 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.79
Source: HOMO SAPIENS
Molecule: Transcription elongation factor B polypeptide 2; Transcription elongation factor B…
UniProt: Q15370, Q15369, P40337
Ligands: ZTD
Pockets: 9 · best druggability 0.60

Structure

x-ray diffraction · resolution 2.79 · 9 distinct chains · 26% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transcription elongation factor B polypeptide 2	protein	102	12% helix, 33% strand	Q15370
B	Transcription elongation factor B polypeptide 1	protein	86	44% helix, 15% strand	Q15369
C	Von hippel-lindau disease tumor suppressor	protein	139	22% helix, 31% strand	P40337
D	Transcription elongation factor B polypeptide 2	protein	100	15% helix, 32% strand	Q15370
E, K	Transcription elongation factor B polypeptide 1	protein	87	44% helix, 15% strand	Q15369
F, I, L	Von hippel-lindau disease tumor suppressor	protein	142	20% helix, 30% strand	P40337
G	Transcription elongation factor B polypeptide 2	protein	102	22% helix, 30% strand	Q15370
H	Transcription elongation factor B polypeptide 1	protein	87	48% helix, 15% strand	Q15369
J	Transcription elongation factor B polypeptide 2	protein	104	18% helix, 33% strand	Q15370

Ligands and binding sites

ZTD · Methyl 4-[({(4R)-4-hydroxy-1-[(3-methylisoxazol-5-yl)acetyl]-L-prolyl}amino)methyl]benzoate · 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	306	0.60	0.78	42	empty
2	238	0.56	0.77	29	ZTD
3	86	0.55	0.85	22	empty
4	87	0.52	0.83	23	empty
5	181	0.45	0.74	24	empty

Interfaces

18 interfaces between chains.

J–K · 1132 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1091 Å² buried · 16 hydrogen bonds · protein-protein
E–F · 1071 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 1067 Å² buried · 10 hydrogen bonds · protein-protein
G–H · 1057 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

3ZTD · PVHL54-213-elob-eloc complex _ methyl 4-(((2S,4R)-4-hydroxy… · 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 3ZTD · PDBe 3ZTD · UniProt Q15370 · UniProt Q15369 · UniProt P40337

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