Research workbench
The molecular architecture of the tramp complex reveals the organization and interplay of its two catalytic activities
Analyse The molecular architecture of the tramp complex reveals the organization and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4U4C
- Type
- protein
- Length
- 980 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent RNA helicase DOB1; Protein AIR2,POLY(A) RNA polymerase protein 2
- EC
- 3.6.4.13, 2.7.7.-
- UniProt
- P47047, Q12476, P53632
- Ligands
- SO4, CL
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent RNA helicase DOB1 (EC 3.6.4.13) | protein | 924 | 50% helix, 16% strand | P47047 |
| B | Protein AIR2,POLY(A) RNA polymerase protein 2 (EC 2.7.7.-) | protein | 56 | 20% helix, 9% strand | Q12476, P53632 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 970 | 0.84 | 0.85 | 103 | SO4 |
| 2 | 520 | 0.72 | 0.81 | 53 | CL |
| 3 | 169 | 0.50 | 0.77 | 28 | empty |
| 4 | 131 | 0.49 | 0.79 | 30 | empty |
| 5 | 149 | 0.45 | 0.76 | 23 | SO4 |
Interfaces
1 interface between chains.
- A–B · 1888 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 4U4C · The molecular architecture of the TRAMP complex reveals the organization and interplay of… · the same entry in another collection · chain A against A, TM-score 1.00
- P47047 · AlphaFold monomer V2.0 prediction for ATP-dependent RNA helicase DOB1 (P47047) · a predicted model of the same protein · chain A against A, TM-score 0.96
- Q12476 · AlphaFold monomer V2.0 prediction for protein AIR2 (Q12476) · a predicted model of the same protein · chain B against A, TM-score 0.36
- P53632 · AlphaFold monomer V2.0 prediction for POLY(A) RNA polymerase protein 2 (P53632) · a predicted model of the same protein · chain B against A, TM-score 0.28
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 P47047
- Every structure of UniProt Q12476
- Every structure of UniProt P53632
- Elsewhere: RCSB PDB 4U4C · PDBe 4U4C · UniProt P47047 · UniProt Q12476 · UniProt P53632
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