MolNFT v1 · #107247 · protein
The molecular architecture of the tramp complex reveals the organization and interplay of its two catalytic activities
4U4C · ATP-dependent RNA helicase DOB1: “The molecular architecture of the tramp complex reveals the organization and interplay of its two catalytic…”. X-ray diffraction, 2 ligands (SO4, CL), 8 pockets (best druggability 0.84). MolNFT v1…
- 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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