MolNFT v1 · #108525 · protein

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

4W9F · Transcription elongation factor B polypeptide 2: “PVHL:ELOB:ELOC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4…”. X-ray diffraction, 1 ligand (3JU), 9 pockets (best druggability 0.72). MolNFT v1 #108525 on GenesisL1: 3D…

PDB: 4W9F
Type: protein
Length: 1,317 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: 3JU
Pockets: 9 · best druggability 0.72

Structure

x-ray diffraction · 11 distinct chains · 29% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transcription elongation factor B polypeptide 2	protein	104	17% helix, 35% strand	Q15370
B	Transcription elongation factor B polypeptide 1	protein	87	48% helix, 15% strand	Q15369
C	Von hippel-lindau disease tumor suppressor	protein	141	24% helix, 30% strand	P40337
D	Transcription elongation factor B polypeptide 2	protein	99	15% helix, 34% strand	Q15370
E	Transcription elongation factor B polypeptide 1	protein	87	45% helix, 15% strand	Q15369
F	Von hippel-lindau disease tumor suppressor	protein	142	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	48% helix, 15% strand	Q15369
I	Von hippel-lindau disease tumor suppressor	protein	144	26% helix, 29% strand	P40337
K	Transcription elongation factor B polypeptide 1	protein	87	45% helix, 15% strand	Q15369
L	Von hippel-lindau disease tumor suppressor	protein	133	20% helix, 32% strand	P40337

Ligands and binding sites

3JU · (4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-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

9 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	64	0.72	0.97	25	empty
2	150	0.52	0.79	18	empty
3	170	0.48	0.76	23	3JU
4	165	0.46	0.76	30	empty
5	166	0.44	0.75	25	empty

Interfaces

14 interfaces between chains.

G–H · 1150 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 1116 Å² buried · 13 hydrogen bonds · protein-protein
J–K · 1113 Å² buried · 13 hydrogen bonds · protein-protein
E–F · 1081 Å² buried · 12 hydrogen bonds · protein-protein
H–I · 1054 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 11 modified (artifact).

Compared structures

4W9F · pVHL:EloB:EloC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylth… · the same entry in another collection · chain K against K, 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 4W9F · PDBe 4W9F · UniProt Q15370 · UniProt Q15369 · UniProt P40337

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