Research workbench

Human tfiib-related factor 2 (BRF2) and tbp bound to U6#2 promoter

Analyse Human tfiib-related factor 2 (BRF2) and tbp bound to U6#2 promoter in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4ROC
Type: protein + DNA
Length: 534 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transcription factor iiib 50 kda subunit; Tata-box-binding protein; Template strand…
UniProt: Q9HAW0, P20226
Ligands: MG
Pockets: 7 · best druggability 0.73

Structure

x-ray diffraction · 4 distinct chains · 49% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transcription factor iiib 50 kda subunit	protein	302	62% helix, 1% strand	Q9HAW0
B	Tata-box-binding protein	protein	178	26% helix, 38% strand	P20226
N	Template strand	dna	27	—	—
T	Non-template strand	dna	27	—	—

Ligands and binding sites

MG · Magnesium ion · metal

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

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1067	0.73	0.77	70	MG
2	673	0.66	0.75	47	empty
3	255	0.55	0.77	27	empty
4	141	0.52	0.80	18	empty
5	200	0.45	0.74	33	empty

Interfaces

6 interfaces between chains.

A–B · 2074 Å² buried · 33 hydrogen bonds · protein-protein
N–T · 1178 Å² buried · 112 hydrogen bonds · nucleic-nucleic
B–T · 868 Å² buried · 11 hydrogen bonds · protein-nucleic
B–N · 774 Å² buried · 5 hydrogen bonds · protein-nucleic
A–N · 610 Å² buried · 7 hydrogen bonds · protein-nucleic

Compared structures

4ROC · Human TFIIB-related factor 2 (Brf2) and TBP bound to U6#2 promoter · the same entry in another collection · chain A against A, TM-score 1.00
P20226 · AlphaFold monomer V2.0 prediction for tata-box-binding protein (P20226) · a predicted model of the same protein · chain B against A, TM-score 0.98
Q9HAW0 · AlphaFold monomer V2.0 prediction for transcription factor iiib 50 kda subunit (Q9HAW0) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q9HAW0
Every structure of UniProt P20226
Elsewhere: RCSB PDB 4ROC · PDBe 4ROC · UniProt Q9HAW0 · UniProt P20226

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