Research workbench
Structure of human TUT7 catalytic module (cm) in complex with dsrna
Analyse Structure of human TUT7 catalytic module (cm) in complex with dsrna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W0O
- Type
- protein + RNA
- Length
- 685 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Terminal uridylyltransferase 7; Double-stranded RNA
- EC
- 2.7.7.52
- UniProt
- Q5VYS8
- Ligands
- UTP
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Terminal uridylyltransferase 7 (EC 2.7.7.52) | protein | 338 | 44% helix, 13% strand | Q5VYS8 |
| B | Terminal uridylyltransferase 7 (EC 2.7.7.52) | protein | 317 | 44% helix, 14% strand | Q5VYS8 |
| C, D | Double-stranded RNA | rna | 15 | — | — |
Ligands and binding sites
- UTP · Uridine 5'-triphosphate · ligand · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 642 | 0.76 | 0.82 | 68 | UTP |
| 2 | 574 | 0.74 | 0.82 | 63 | UTP |
| 3 | 80 | 0.40 | 0.78 | 15 | empty |
| 4 | 131 | 0.39 | 0.74 | 23 | empty |
| 5 | 162 | 0.38 | 0.73 | 15 | empty |
Interfaces
5 interfaces between chains.
- C–D · 675 Ų buried · 73 hydrogen bonds · nucleic-nucleic
- B–D · 574 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–C · 479 Ų buried · 4 hydrogen bonds · protein-nucleic
- B–C · 269 Ų buried · 2 hydrogen bonds · protein-nucleic
- A–D · 229 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 5W0O · Structure of human TUT7 catalytic module (CM) in complex with dsRNA · the same entry in another collection · chain A against A, TM-score 1.00
- Q5VYS8 · AlphaFold monomer V2.0 prediction for terminal uridylyltransferase 7 (Q5VYS8) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q5VYS8
- Elsewhere: RCSB PDB 5W0O · PDBe 5W0O · UniProt Q5VYS8
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