Research workbench

Model for VP16 binding to tfiib

Analyse Model for VP16 binding to tfiib in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2PHG
Type: protein
Length: 232 residues
Chains: 2
Method: solution nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transcription initiation factor iib; Alpha trans-inducing protein
UniProt: Q00403, P06492
Pockets: 2 · best druggability 0.54

Structure

solution nmr · 2 distinct chains · 51% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transcription initiation factor iib	protein	206	51% helix, 0% strand	Q00403
B	Alpha trans-inducing protein	protein	26	46% helix, 0% strand	P06492

Pockets

2 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	173	0.54	0.79	30	empty
2	105	0.48	0.80	19	empty

Interfaces

1 interface between chains.

A–B · 1017 Å² buried · 36 hydrogen bonds · protein-protein

Compared structures

2PHG · Model for VP16 binding to TFIIB · the same entry in another collection · chain A against A, TM-score 1.00
Q00403 · AlphaFold monomer V2.0 prediction for transcription initiation factor iib (Q00403) · a predicted model of the same protein · chain A against A, TM-score 0.52

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 Q00403
Every structure of UniProt P06492
Elsewhere: RCSB PDB 2PHG · PDBe 2PHG · UniProt Q00403 · UniProt P06492

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