Research workbench

PVHL:ELOB:ELOC in complex with (2S,4R)-1-((S)-2-((S)-2-acetamido-3- phenylpropanamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4- methylthiazol-5-YL)BENZYL)PYRROLIDINE-2-carboxamide (ligand 14)

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

PDB: 4W9K
Type: protein
Length: 1,331 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: 3JO
Pockets: 8 · best druggability 0.63

Structure

x-ray diffraction · 9 distinct chains · 28% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G, J	Transcription elongation factor B polypeptide 2	protein	103	15% helix, 39% strand	Q15370
B	Transcription elongation factor B polypeptide 1	protein	86	49% helix, 15% strand	Q15369
C	Von hippel-lindau disease tumor suppressor	protein	141	26% helix, 30% strand	P40337
D	Transcription elongation factor B polypeptide 2	protein	102	15% helix, 37% strand	Q15370
E, H	Transcription elongation factor B polypeptide 1	protein	88	44% helix, 15% strand	Q15369
F	Von hippel-lindau disease tumor suppressor	protein	144	27% helix, 29% strand	P40337
I	Von hippel-lindau disease tumor suppressor	protein	142	23% helix, 30% strand	P40337
K	Transcription elongation factor B polypeptide 1	protein	88	48% helix, 15% strand	Q15369
L	Von hippel-lindau disease tumor suppressor	protein	143	21% helix, 29% strand	P40337

Ligands and binding sites

3JO · N-acetyl-L-phenylalanyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide · 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	274	0.63	0.80	43	3JO
2	234	0.62	0.81	36	3JO
3	164	0.44	0.75	28	empty
4	132	0.38	0.73	24	empty
5	133	0.36	0.73	23	empty

Interfaces

18 interfaces between chains.

G–H · 1141 Å² buried · 12 hydrogen bonds · protein-protein
J–K · 1138 Å² buried · 13 hydrogen bonds · protein-protein
D–E · 1131 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1125 Å² buried · 14 hydrogen bonds · protein-protein
E–F · 1043 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified (artifact).

Compared structures

4W9K · pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-((S)-2-acetamido-3-phenylpropanamido)-3,3… · 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 4W9K · PDBe 4W9K · UniProt Q15370 · UniProt Q15369 · UniProt P40337

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