Research workbench

Pvhl-elob-eloc COMPLEX_(2S,4R)-1-(3-amino-2-methylbenzoyl)-4- hydroxy-N-(4-(4-methylthiazol-5-YL)BENZYL) pyrrolidine-2-carboxamide bound

Analyse Pvhl-elob-eloc COMPLEX_(2S,4R)-1-(3-amino-2-methylbenzoyl)-4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4B9K
Type: protein
Length: 1,339 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: TG0
Pockets: 14 · best druggability 0.53

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transcription elongation factor B polypeptide 2	protein	103	17% helix, 37% strand	Q15370
B	Transcription elongation factor B polypeptide 1	protein	88	44% 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	101	15% helix, 36% strand	Q15370
E	Transcription elongation factor B polypeptide 1	protein	87	44% helix, 15% strand	Q15369
F	Von hippel-lindau disease tumor suppressor	protein	143	27% helix, 29% 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	89	48% helix, 15% strand	Q15369
I	Von hippel-lindau disease tumor suppressor	protein	147	25% helix, 29% strand	P40337
K	Transcription elongation factor B polypeptide 1	protein	91	46% helix, 14% strand	Q15369
L	Von hippel-lindau disease tumor suppressor	protein	146	24% helix, 29% strand	P40337

Ligands and binding sites

TG0 · (2S,4R)-1-(3-amino-2-methylbenzoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide · ligand · 4 copies · chains C, F, I, L
ACT · Acetate ion · additive · 8 copies · chains F, H, I, J, K, L

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

Pockets

14 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	80	0.53	0.84	22	ACT
2	59	0.51	0.86	18	empty
3	186	0.50	0.76	22	TG0
4	169	0.48	0.76	22	TG0
5	143	0.43	0.76	25	empty

Interfaces

15 interfaces between chains.

J–K · 1159 Å² buried · 14 hydrogen bonds · protein-protein
G–H · 1153 Å² buried · 13 hydrogen bonds · protein-protein
D–E · 1153 Å² buried · 13 hydrogen bonds · protein-protein
K–L · 1139 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 1137 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 13 modified (artifact).

Compared structures

4B9K · pVHL-ELOB-ELOC complex_(2S,4R)-1-(3-amino-2-methylbenzoyl)-4-hydroxy-N-(4-(4-methylthiazol… · 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 4B9K · PDBe 4B9K · UniProt Q15370 · UniProt Q15369 · UniProt P40337

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