MolNFT v1 · #57350 · protein
Crystal structure of H61A mutant TTHA0252 from thermus thermophilus HB8
3A4Y · Ribonuclease TTHA0252: “Crystal structure of H61A mutant TTHA0252 from thermus thermophilus HB8”. X-ray diffraction, 2 ligands (ZN, SO4), 15 pockets (best druggability 0.77). MolNFT v1 #57350 on GenesisL1: 3D structure, binding…
- PDB
- 3A4Y
- 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
- 15 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ribonuclease TTHA0252 (EC 3.1.-.-) | protein | 431 | 33% helix, 23% strand | Q5SLP1 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 56 copies · chains A, D, B, C
- FLC · Citrate anion · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 854 | 0.77 | 0.80 | 61 | SO4 |
| 2 | 917 | 0.76 | 0.79 | 61 | SO4 |
| 3 | 940 | 0.76 | 0.79 | 63 | SO4 |
| 4 | 577 | 0.75 | 0.82 | 69 | SO4 |
| 5 | 873 | 0.74 | 0.78 | 61 | SO4 |
Interfaces
4 interfaces between chains.
- A–D · 1242 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 937 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 694 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 16 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3A4Y · Crystal Structure of H61A mutant TTHA0252 from Thermus thermophilus HB8 · the same entry in another collection · chain B against B, 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 3A4Y · PDBe 3A4Y · UniProt Q5SLP1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.