MolNFT v1 · #67241 · protein + RNA
Crystal structure of TTHA0252 from thermus thermophilus HB8 complexed with RNA analog
3IEM · Ribonuclease TTHA0252: “Crystal structure of TTHA0252 from thermus thermophilus HB8 complexed with RNA analog”. X-ray diffraction, 3 ligands (ZN, SO4, SSU), 20 pockets (best druggability 0.78). MolNFT v1 #67241 on GenesisL1: 3D…
- 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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