Research workbench

Xpb-containing part of tfiih in a post-translocated state (with ADP- BEF3)

Analyse Xpb-containing part of tfiih in a post-translocated state (with ADP- BEF3) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7NVV
Type: protein + DNA
Length: 1,049 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: General transcription factor iih subunit 4; General transcription factor iih subunit 5…
EC: 3.6.4.12
UniProt: Q92759, Q6ZYL4, P19447, P29083
Ligands: ADP, BEF, MG
Pockets: 14 · best druggability 0.80

Structure

electron microscopy · 8 distinct chains · 44% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
2	General transcription factor iih subunit 4	protein	289	55% helix, 15% strand	Q92759
5	General transcription factor iih subunit 5	protein	66	45% helix, 24% strand	Q6ZYL4
7	General transcription and DNA repair factor iih helicase subunit xpb (EC 3.6.4.12)	protein	605	40% helix, 20% strand	P19447
N	Non-template DNA	dna	25	—	—
T	Template DNA	dna	25	—	—
W	General transcription factor iie subunit 1	protein	15	27% helix, 0% strand	P29083
Y	Unassigned peptide, likely xpb	protein	8	0% helix, 13% strand	—
Z	Unassigned peptide, likely tfiie-beta	protein	16	0% helix, 0% strand	—

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · chains 7
BEF · Beryllium trifluoride ion · ligand · chains 7
MG · Magnesium ion · metal · chains 7

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

Pockets

14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	267	0.80	0.93	35	empty
2	843	0.80	0.83	99	empty
3	225	0.70	0.87	28	empty
4	209	0.64	0.84	33	ADP, MG, BEF
5	516	0.63	0.76	42	empty

Interfaces

11 interfaces between chains.

2–7 · 1381 Å² buried · 16 hydrogen bonds · protein-protein
2–5 · 1269 Å² buried · 20 hydrogen bonds · protein-protein
N–T · 1131 Å² buried · 80 hydrogen bonds · nucleic-nucleic
5–7 · 714 Å² buried · 8 hydrogen bonds · protein-protein
7–T · 685 Å² buried · 10 hydrogen bonds · protein-nucleic

Compared structures

7NVV · XPB-containing part of TFIIH in a post-translocated state (with ADP-BeF3) · the same entry in another collection · chain Z against Z, TM-score 1.00
P19447 · 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 0.89
Q92759 · AlphaFold monomer V2.0 prediction for general transcription factor iih subunit 4 (Q92759) · a predicted model of the same protein · chain 2 against A, TM-score 0.77
Q6ZYL4 · AlphaFold monomer V2.0 prediction for general transcription factor iih subunit 5 (Q6ZYL4) · a predicted model of the same protein · chain 5 against A, TM-score 0.74
P29083 · AlphaFold monomer V2.0 prediction for general transcription factor iie subunit 1 (P29083) · a predicted model of the same protein · chain W against A, TM-score 0.41

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 Q92759
Every structure of UniProt Q6ZYL4
Every structure of UniProt P19447
Every structure of UniProt P29083
Elsewhere: RCSB PDB 7NVV · PDBe 7NVV · UniProt Q92759 · UniProt Q6ZYL4 · UniProt P19447 · UniProt P29083

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