MolNFT v1 · #108527 · protein

PVHL:ELOB:ELOC in complex with (2S,4R)-1-((S)-2-acetamido-3,3- dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-YL)BENZYL) pyrrolidine-2-carboxamide (ligand 7)

4W9H · Transcription elongation factor B polypeptide 2: “PVHL:ELOB:ELOC in complex with (2S,4R)-1-((S)-2-acetamido-3,3…”. X-ray diffraction, 1 ligand (3JF), 7 pockets (best druggability 0.58). MolNFT v1 #108527 on GenesisL1: 3D structure…

PDB: 4W9H
Type: protein
Length: 1,332 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: 3JF
Pockets: 7 · best druggability 0.58

Structure

x-ray diffraction · 8 distinct chains · 29% 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	45% 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	26% helix, 29% strand	P40337
I, L	Von hippel-lindau disease tumor suppressor	protein	143	25% helix, 29% strand	P40337
K	Transcription elongation factor B polypeptide 1	protein	88	48% helix, 15% strand	Q15369

Ligands and binding sites

3JF · N-acetyl-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

7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	218	0.58	0.79	40	3JF
2	226	0.50	0.75	34	3JF
3	155	0.45	0.76	25	empty
4	149	0.44	0.76	24	empty
5	130	0.38	0.74	23	empty

Interfaces

17 interfaces between chains.

J–K · 1142 Å² buried · 14 hydrogen bonds · protein-protein
G–H · 1141 Å² buried · 15 hydrogen bonds · protein-protein
D–E · 1132 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 1130 Å² buried · 14 hydrogen bonds · protein-protein
E–F · 1067 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 modified (artifact).

Compared structures

4W9H · pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-acetamido-3,3-dimethylbutanoyl)-4-hydroxy… · 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 4W9H · PDBe 4W9H · UniProt Q15370 · UniProt Q15369 · UniProt P40337

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