Research workbench
Crystal structure of H380A mutant TTHA0252 from thermus thermophilus HB8 complexed with RNA
Analyse Crystal structure of H380A mutant TTHA0252 from thermus thermophilus HB8… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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