Research workbench
Structure of human TUT7 catalytic module (cm) in complex with U5 RNA
Analyse Structure of human TUT7 catalytic module (cm) in complex with U5 RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W0M
- Type
- protein + RNA
- Length
- 1,105 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Terminal uridylyltransferase 7; U5 single-stranded RNA
- EC
- 2.7.7.52
- UniProt
- Q5VYS8
- Ligands
- ZN, SO4, IOD
- Pockets
- 17 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Terminal uridylyltransferase 7 (EC 2.7.7.52) | protein | 372 | 44% helix, 12% strand | Q5VYS8 |
| B | Terminal uridylyltransferase 7 (EC 2.7.7.52) | protein | 350 | 44% helix, 13% strand | Q5VYS8 |
| C | Terminal uridylyltransferase 7 (EC 2.7.7.52) | protein | 371 | 43% helix, 12% strand | Q5VYS8 |
| H, I, J | U5 single-stranded RNA | rna | 4 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · 4 copies · chains A, H, B, C, I, J
- IOD · Iodide ion · ion · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 678 | 0.84 | 0.88 | 62 | SO4 |
| 2 | 309 | 0.73 | 0.86 | 36 | SO4 |
| 3 | 283 | 0.72 | 0.86 | 34 | SO4 |
| 4 | 680 | 0.72 | 0.79 | 73 | empty |
| 5 | 264 | 0.66 | 0.83 | 46 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1164 Ų buried · 5 hydrogen bonds · protein-protein
- A–H · 829 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–C · 810 Ų buried · 5 hydrogen bonds · protein-protein
- C–J · 789 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–I · 750 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 5W0M · Structure of human TUT7 catalytic module (CM) in complex with U5 RNA · the same entry in another collection · chain J against J, TM-score 1.00
- Q5VYS8 · AlphaFold monomer V2.0 prediction for terminal uridylyltransferase 7 (Q5VYS8) · a predicted model of the same protein · chain A against A, 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 Q5VYS8
- Elsewhere: RCSB PDB 5W0M · PDBe 5W0M · UniProt Q5VYS8
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