MolNFT v1 · #183834 · protein + DNA
Yeast tfiih in the expanded state within the pre-initiation complex
7O4L · General transcription and DNA repair factor iih helicase…: “Yeast tfiih in the expanded state within the pre-initiation complex”. Electron microscopy, 5 ligands (SF4, BEF, ADP), 20 pockets (best druggability 0.84). MolNFT v1 #183834…
- PDB
- 7O4L
- Type
- protein + DNA
- Length
- 4,350 residues
- Chains
- 17
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- General transcription and DNA repair factor iih helicase subunit xpd; General…
- EC
- 3.6.4.12, 2.7.7.6
- UniProt
- P06839, P32776, Q02939, Q03290, Q12004, Q3E7C1, Q04673, Q00578, P04050, P08518, P20433, P20435, P34087, P36100, P36145
- Ligands
- SF4, BEF, ADP, ZN, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 17 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 0 | General transcription and DNA repair factor iih helicase subunit xpd (EC 3.6.4.12) | protein | 752 | 50% helix, 14% strand | P06839 |
| 1 | General transcription and DNA repair factor iih subunit TFB1 | protein | 521 | 55% helix, 10% strand | P32776 |
| 2 | General transcription and DNA repair factor iih subunit TFB2 | protein | 445 | 53% helix, 15% strand | Q02939 |
| 3 | RNA polymerase II transcription factor B subunit 3 | protein | 131 | 46% helix, 10% strand | Q03290 |
| 4 | General transcription and DNA repair factor iih subunit TFB4 | protein | 293 | 40% helix, 17% strand | Q12004 |
| 5 | General transcription and DNA repair factor iih subunit TFB5 | protein | 65 | 48% helix, 28% strand | Q3E7C1 |
| 6 | General transcription and DNA repair factor iih subunit SSL1 | protein | 374 | 33% helix, 20% strand | Q04673 |
| 7 | General transcription and DNA repair factor iih helicase subunit xpb (EC 3.6.4.12) | protein | 607 | 40% helix, 17% strand | Q00578 |
| A | DNA-directed RNA polymerase II subunit RPB1 (EC 2.7.7.6) | protein | 227 | 33% helix, 14% strand | P04050 |
| B | DNA-directed RNA polymerase II subunit RPB2 (EC 2.7.7.6) | protein | 81 | 27% helix, 30% strand | P08518 |
| D | DNA-directed RNA polymerase II subunit RPB4 | protein | 162 | 56% helix, 7% strand | P20433 |
| F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | protein | 55 | 44% helix, 16% strand | P20435 |
| G | DNA-directed RNA polymerase II subunit RPB7 | protein | 171 | 11% helix, 51% strand | P34087 |
| N | Nontemplate DNA | dna | 10 | — | — |
| T | Template DNA | dna | 10 | — | — |
| W | Transcription initiation factor iie subunit alpha | protein | 311 | 50% helix, 11% strand | P36100 |
| X | Transcription initiation factor iie subunit beta | protein | 135 | 33% helix, 9% strand | P36145 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains 0
- BEF · Beryllium trifluoride ion · ligand · chains 7
- ADP · Adenosine-5'-diphosphate · ligand · chains 7
- ZN · Zinc ion · metal · 11 copies · chains 3, 4, 6, A, B, W
- MG · Magnesium ion · metal · chains 7
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 225 | 0.84 | 0.97 | 32 | empty |
| 2 | 1035 | 0.80 | 0.82 | 90 | empty |
| 3 | 860 | 0.79 | 0.82 | 65 | empty |
| 4 | 559 | 0.78 | 0.85 | 52 | empty |
| 5 | 802 | 0.78 | 0.81 | 76 | empty |
Interfaces
42 interfaces between chains.
- 0–1 · 4138 Ų buried · 43 hydrogen bonds · protein-protein
- 1–4 · 3035 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 2833 Ų buried · 41 hydrogen bonds · protein-protein
- 4–6 · 2588 Ų buried · 20 hydrogen bonds · protein-protein
- 1–W · 2462 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 7O4L · Yeast TFIIH in the expanded state within the pre-initiation complex · the same entry in another collection · chain D against D, 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 P06839
- Every structure of UniProt P32776
- Every structure of UniProt Q02939
- Every structure of UniProt Q03290
- Every structure of UniProt Q12004
- Every structure of UniProt Q3E7C1
- Every structure of UniProt Q04673
- Every structure of UniProt Q00578
- Every structure of UniProt P04050
- Every structure of UniProt P08518
- Every structure of UniProt P20433
- Every structure of UniProt P20435
- Every structure of UniProt P34087
- Every structure of UniProt P36100
- Every structure of UniProt P36145
- Elsewhere: RCSB PDB 7O4L · PDBe 7O4L · UniProt P06839 · UniProt P32776 · UniProt Q02939 · UniProt Q03290 · UniProt Q12004 · UniProt Q3E7C1 · UniProt Q04673 · UniProt Q00578 · UniProt P04050 · UniProt P08518 · UniProt P20433 · UniProt P20435 · UniProt P34087 · UniProt P36100 · UniProt P36145
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