Research workbench
Crystal structure of TTHA0252 from thermus thermophilus HB8 complexed with ump
Analyse Crystal structure of TTHA0252 from thermus thermophilus HB8 complexed with ump in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IEL
- 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
- U5P, ZN, SO4
- Pockets
- 16 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ribonuclease TTHA0252 (EC 3.1.-.-) | protein | 431 | 35% helix, 22% strand | Q5SLP1 |
Ligands and binding sites
- U5P · Uridine-5'-monophosphate · ligand · 7 copies · chains A, D, B, C
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 96 copies · chains A, D, B, C
- FLC · Citrate anion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 950 | 0.78 | 0.80 | 80 | SO4, U5P |
| 2 | 921 | 0.77 | 0.80 | 71 | SO4, U5P, ZN |
| 3 | 865 | 0.77 | 0.80 | 57 | SO4, U5P |
| 4 | 842 | 0.76 | 0.80 | 75 | SO4, U5P, ZN |
| 5 | 570 | 0.75 | 0.82 | 68 | SO4 |
Interfaces
3 interfaces between chains.
- A–D · 1202 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 979 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 787 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 3IEL · Crystal Structure of TTHA0252 from Thermus thermophilus HB8 complexed with UMP · 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 3IEL · PDBe 3IEL · UniProt Q5SLP1
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