Research workbench
Crystal structure of S378Q mutant TTHA0252 from thermus thermophilus HB8
Analyse Crystal structure of S378Q 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
- 3IDZ
- Type
- protein
- Length
- 1,724 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease TTHA0252
- EC
- 3.1.-.-
- UniProt
- Q5SLP1
- Ligands
- ZN, SO4
- Pockets
- 18 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ribonuclease TTHA0252 (EC 3.1.-.-) | protein | 431 | 34% helix, 21% strand | Q5SLP1 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 66 copies · chains A, D, B, C
- FLC · Citrate anion · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 814 | 0.77 | 0.80 | 67 | SO4 |
| 2 | 921 | 0.76 | 0.79 | 73 | SO4 |
| 3 | 812 | 0.75 | 0.80 | 62 | SO4, FLC |
| 4 | 855 | 0.75 | 0.79 | 67 | SO4 |
| 5 | 499 | 0.73 | 0.82 | 65 | SO4 |
Interfaces
4 interfaces between chains.
- A–D · 1226 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 956 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 732 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 23 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3IDZ · Crystal Structure of S378Q mutant TTHA0252 from Thermus thermophilus HB8 · the same entry in another collection · chain A against A, 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 3IDZ · PDBe 3IDZ · UniProt Q5SLP1
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