Research workbench

Von hippel lindau PROTEIN:ELONGINB:ELONGINC complex, in complex with (2S,4R)-N-methyl-1-[2-(3-methyl-1,2-oxazol-5-YL)ETHANOYL]-4-oxidanyl- pyrrolidine-2-carboxamide

Analyse Von hippel lindau PROTEIN:ELONGINB:ELONGINC complex, in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4BKT
Type: protein
Length: 1,326 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: QD0, GLU, ARG
Pockets: 8 · best druggability 0.59

Structure

x-ray diffraction · 10 distinct chains · 27% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transcription elongation factor B polypeptide 2	protein	104	14% helix, 37% strand	Q15370
B, E	Transcription elongation factor B polypeptide 1	protein	87	48% helix, 15% strand	Q15369
C	Von hippel-lindau disease tumor suppressor	protein	138	22% helix, 30% strand	P40337
D	Transcription elongation factor B polypeptide 2	protein	102	15% helix, 35% strand	Q15370
F	Von hippel-lindau disease tumor suppressor	protein	141	27% helix, 30% strand	P40337
G, J	Transcription elongation factor B polypeptide 2	protein	103	15% helix, 39% strand	Q15370
H	Transcription elongation factor B polypeptide 1	protein	87	47% helix, 15% strand	Q15369
I	Von hippel-lindau disease tumor suppressor	protein	143	25% helix, 29% strand	P40337
K	Transcription elongation factor B polypeptide 1	protein	87	47% helix, 15% strand	Q15369
L	Von hippel-lindau disease tumor suppressor	protein	144	24% helix, 29% strand	P40337

Ligands and binding sites

QD0 · (2S,4R)-N-methyl-1-[2-(3-methyl-1,2-oxazol-5-yl)ethanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide · ligand · 4 copies · chains C, F, I, L
GLU · Glutamic acid · ligand · chains F
ARG · Arginine · ligand · chains 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	234	0.59	0.79	36	QD0
2	213	0.57	0.79	34	empty
3	82	0.52	0.84	20	empty
4	146	0.42	0.75	23	empty
5	159	0.42	0.74	24	empty

Interfaces

16 interfaces between chains.

J–K · 1151 Å² buried · 15 hydrogen bonds · protein-protein
G–H · 1146 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1141 Å² buried · 14 hydrogen bonds · protein-protein
E–F · 1101 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 1088 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified, 2 covalent (artifact, covalent ligand).

Compared structures

4BKT · von Hippel Lindau protein:ElonginB:ElonginC complex, in complex with… · 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 4BKT · PDBe 4BKT · UniProt Q15370 · UniProt Q15369 · UniProt P40337

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.