Research workbench
Crystal structure of TTHA0252 from thermus thermophilus HB8 complexed with RNA analog
Analyse Crystal structure of TTHA0252 from thermus thermophilus HB8 complexed with RNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IEM
- Type
- protein + RNA
- Length
- 1,747 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease TTHA0252; RNA (5'-R(*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU))-3')
- EC
- 3.1.-.-
- UniProt
- Q5SLP1
- Ligands
- ZN, SO4, SSU
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ribonuclease TTHA0252 (EC 3.1.-.-) | protein | 431 | 34% helix, 22% strand | Q5SLP1 |
| G | RNA (5'-R(*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU))-3') | rna | 5 | — | — |
| H, K | RNA (5'-R(*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU))-3') | rna | 3 | — | — |
| I | RNA (5'-R(*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU))-3') | rna | 4 | — | — |
| J, L, N, O | RNA (5'-R(*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU))-3') | rna | 2 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, G, B, K, C, D, I
- SO4 · Sulfate ion · ion · 59 copies · chains A, D, G, B, K, L, C, J
- SSU · Uridine-5'-phosphorothioate · ion · 12 copies · chains A, G, H, D, I, J, L, N, C, O
- FLC · Citrate anion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 596 | 0.78 | 0.84 | 71 | SSU, SO4, ZN |
| 2 | 587 | 0.75 | 0.82 | 68 | SO4 |
| 3 | 546 | 0.72 | 0.81 | 43 | SO4 |
| 4 | 65 | 0.70 | 0.96 | 22 | SO4 |
| 5 | 272 | 0.60 | 0.79 | 31 | empty |
Interfaces
13 interfaces between chains.
- A–D · 1224 Ų buried · 22 hydrogen bonds · protein-protein
- A–G · 1088 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–C · 1036 Ų buried · 14 hydrogen bonds · protein-protein
- D–I · 960 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–B · 757 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 23 modified, 2 covalent (nucleotide modification, covalent ligand).
Compared structures
- 3IEM · Crystal Structure of TTHA0252 from Thermus thermophilus HB8 complexed with RNA analog · the same entry in another collection · chain K against K, 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 0.99
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 3IEM · PDBe 3IEM · UniProt Q5SLP1
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