Research workbench

General transcription factor tfiih (weak binding)

Analyse General transcription factor tfiih (weak binding) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7ML3
Type: protein + DNA
Length: 3,028 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BJ4_G0050160.MRNA.1.CDS.1; RNA polymerase II transcription factor B subunit 2; General…
EC: 3.6.4.12
UniProt: A0A7I9BTI9, A0A6A5Q2X3, A0A6A5Q1C1, A0A7I9C5C2, A0A7I9FQL5, Q3E7C1, Q00578
Ligands: SF4, ZN
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 10 distinct chains · 45% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
3	BJ4_G0050160.MRNA.1.CDS.1	protein	138	43% helix, 1% strand	A0A7I9BTI9
2	RNA polymerase II transcription factor B subunit 2	protein	460	49% helix, 5% strand	A0A6A5Q2X3
0	General transcription and DNA repair factor iih helicase subunit xpd (EC 3.6.4.12)	protein	754	51% helix, 10% strand	A0A6A5Q1C1
1	TFB1	protein	367	67% helix, 0% strand	—
4	General transcription and DNA repair factor iih subunit TFB4	protein	284	35% helix, 13% strand	A0A7I9C5C2
6	General transcription and DNA repair factor iih	protein	351	28% helix, 13% strand	A0A7I9FQL5
5	General transcription and DNA repair factor iih subunit TFB5	protein	66	44% helix, 21% strand	Q3E7C1
7	General transcription and DNA repair factor iih helicase subunit xpb (EC 3.6.4.12)	protein	548	37% helix, 11% strand	Q00578
N	Non-template strand DNA	dna	30	—	—
T	Template strand DNA	dna	30	—	—

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · chains 0
ZN · Zinc ion · metal · 7 copies · chains 3, 4, 6

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	939	0.85	0.86	108	empty
2	757	0.82	0.85	97	empty
3	725	0.81	0.84	77	empty
4	527	0.80	0.86	97	empty
5	520	0.77	0.84	57	empty

Interfaces

17 interfaces between chains.

0–1 · 2330 Å² buried · 33 hydrogen bonds · protein-protein
4–6 · 1730 Å² buried · 16 hydrogen bonds · protein-protein
N–T · 1391 Å² buried · 110 hydrogen bonds · nucleic-nucleic
1–6 · 1129 Å² buried · 11 hydrogen bonds · protein-protein
2–5 · 927 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

7ML3 · General transcription factor TFIIH (weak binding) · the same entry in another collection · chain N against N, TM-score 1.00
Q00578 · AlphaFold monomer V2.0 prediction for general transcription and DNA repair factor iih… · a predicted model of the same protein · chain 7 against A, TM-score 0.87
Q3E7C1 · AlphaFold monomer V2.0 prediction for general transcription and DNA repair factor iih… · a predicted model of the same protein · chain 5 against A, TM-score 0.76

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 A0A7I9BTI9
Every structure of UniProt A0A6A5Q2X3
Every structure of UniProt A0A6A5Q1C1
Every structure of UniProt A0A7I9C5C2
Every structure of UniProt A0A7I9FQL5
Every structure of UniProt Q3E7C1
Every structure of UniProt Q00578
Elsewhere: RCSB PDB 7ML3 · PDBe 7ML3 · UniProt A0A7I9BTI9 · UniProt A0A6A5Q2X3 · UniProt A0A6A5Q1C1 · UniProt A0A7I9C5C2 · UniProt A0A7I9FQL5 · UniProt Q3E7C1 · UniProt Q00578

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