Research workbench
Cryo-EM structure of yeast tho complex with SUB2
Analyse Cryo-EM structure of yeast tho complex with SUB2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7V2Y
- Type
- protein
- Length
- 2,846 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tho complex subunit HPR1; Tho complex subunit 2; Protein TEX1; Tho complex subunit MFT1…
- EC
- 3.6.4.13
- UniProt
- P17629, P53552, P53851, P33441, O13539, Q07478
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 6 distinct chains · 47% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tho complex subunit HPR1 | protein | 593 | 51% helix, 0% strand | P17629 |
| B | Tho complex subunit 2 | protein | 1226 | 56% helix, 2% strand | P53552 |
| C | Protein TEX1 | protein | 333 | 3% helix, 35% strand | P53851 |
| D | Tho complex subunit MFT1 | protein | 138 | 74% helix, 0% strand | P33441 |
| E | Tho complex subunit THP2 | protein | 180 | 62% helix, 2% strand | O13539 |
| F | ATP-dependent RNA helicase SUB2 (EC 3.6.4.13) | protein | 376 | 34% helix, 15% strand | Q07478 |
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 | 1085 | 0.85 | 0.86 | 103 | empty |
| 2 | 1045 | 0.84 | 0.85 | 83 | empty |
| 3 | 1175 | 0.83 | 0.84 | 103 | empty |
| 4 | 563 | 0.79 | 0.85 | 55 | empty |
| 5 | 1188 | 0.79 | 0.81 | 92 | empty |
Interfaces
10 interfaces between chains.
- A–B · 7936 Ų buried · 65 hydrogen bonds · protein-protein
- D–E · 3154 Ų buried · 11 hydrogen bonds · protein-protein
- B–F · 2556 Ų buried · 30 hydrogen bonds · protein-protein
- A–E · 2492 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 2172 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 7V2Y · cryo-EM structure of yeast THO complex with Sub2 · the same entry in another collection · chain F against F, TM-score 1.00
- P53851 · AlphaFold monomer V2.0 prediction for protein TEX1 (P53851) · a predicted model of the same protein · chain C against A, TM-score 0.94
- P53552 · AlphaFold monomer V2.0 prediction for tho complex subunit 2 (P53552) · a predicted model of the same protein · chain B against A, TM-score 0.84
- Q07478 · AlphaFold monomer V2.0 prediction for ATP-dependent RNA helicase SUB2 (Q07478) · a predicted model of the same protein · chain F against A, TM-score 0.67
- P33441 · AlphaFold monomer V2.0 prediction for tho complex subunit MFT1 (P33441) · a predicted model of the same protein · chain D against A, TM-score 0.60
- P17629 · AlphaFold monomer V2.0 prediction for tho complex subunit HPR1 (P17629) · a predicted model of the same protein · chain A against A, TM-score 0.43
- O13539 · AlphaFold monomer V2.0 prediction for tho complex subunit THP2 (O13539) · a predicted model of the same protein · chain E against A, TM-score 0.43
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 P17629
- Every structure of UniProt P53552
- Every structure of UniProt P53851
- Every structure of UniProt P33441
- Every structure of UniProt O13539
- Every structure of UniProt Q07478
- Elsewhere: RCSB PDB 7V2Y · PDBe 7V2Y · UniProt P17629 · UniProt P53552 · UniProt P53851 · UniProt P33441 · UniProt O13539 · UniProt Q07478
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