MolNFT v1 · #67222 · protein + RNA
Crystal structure of H380A mutant TTHA0252 from thermus thermophilus HB8 complexed with RNA
3IE1 · Ribonuclease TTHA0252: “Crystal structure of H380A mutant TTHA0252 from thermus thermophilus HB8 complexed with RNA”. X-ray diffraction, 2 ligands (ZN, SO4), 16 pockets (best druggability 0.74). MolNFT v1 #67222 on GenesisL1: 3D…
- PDB
- 3IE1
- Type
- protein + RNA
- Length
- 1,738 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease TTHA0252; RNA (5'-R(P*UP*UP*UP*U)-3')
- EC
- 3.1.-.-
- UniProt
- Q5SLP1
- Ligands
- ZN, SO4
- Pockets
- 16 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ribonuclease TTHA0252 (EC 3.1.-.-) | protein | 431 | 34% helix, 20% strand | Q5SLP1 |
| E, F, H | RNA (5'-R(P*UP*UP*UP*U)-3') | rna | 4 | — | — |
| G | RNA (5'-R(P*UP*UP*UP*U)-3') | rna | 2 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, E, B, F, C, G, D, H
- SO4 · Sulfate ion · ion · 54 copies · chains A, B, E, D, F, C, G
- FLC · Citrate anion · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 768 | 0.74 | 0.79 | 62 | SO4 |
| 2 | 595 | 0.74 | 0.81 | 68 | SO4 |
| 3 | 391 | 0.73 | 0.84 | 51 | SO4 |
| 4 | 382 | 0.72 | 0.83 | 61 | SO4 |
| 5 | 319 | 0.71 | 0.85 | 55 | SO4 |
Interfaces
7 interfaces between chains.
- A–D · 1206 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 994 Ų buried · 9 hydrogen bonds · protein-protein
- B–F · 862 Ų buried · 15 hydrogen bonds · protein-nucleic
- D–H · 847 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–E · 831 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 3IE1 · Crystal structure of H380A mutant TTHA0252 from Thermus thermophilus HB8 complexed with… · the same entry in another collection · chain H against H, TM-score 1.00
- Q5SLP1 · AlphaFold monomer V2.0 prediction for ribonuclease TTHA0252 (Q5SLP1) · 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 Q5SLP1
- Elsewhere: RCSB PDB 3IE1 · PDBe 3IE1 · UniProt Q5SLP1
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