MolNFT v1 · #137827 · protein + RNA
Structure of human TUT7 catalytic module (cm) in complex with U5 RNA
5W0M · Terminal uridylyltransferase 7: “Structure of human TUT7 catalytic module (cm) in complex with U5 RNA”. X-ray diffraction, 3 ligands (ZN, SO4, IOD), 17 pockets (best druggability 0.84). MolNFT v1 #137827 on GenesisL1: 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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