MolNFT v1 · #142562 · protein
Crystal structure of T. gondii prolyl tRNA synthetase with febrifugine and ATP analog
6A88 · Prolyl-tRNA synthetase (prors): “Crystal structure of T. gondii prolyl tRNA synthetase with febrifugine and ATP analog”. X-ray diffraction, 3 ligands (ANP, 9SF, MG), 20 pockets (best druggability 0.83). MolNFT v1 #142562 on…
- PDB
- 6A88
- Type
- protein
- Length
- 1,915 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prolyl-tRNA synthetase (prors)
- EC
- 6.1.1.15
- UniProt
- S8G8I1
- Ligands
- ANP, 9SF, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prolyl-tRNA synthetase (prors) (EC 6.1.1.15) | protein | 482 | 37% helix, 29% strand | S8G8I1 |
| B | Prolyl-tRNA synthetase (prors) (EC 6.1.1.15) | protein | 481 | 37% helix, 29% strand | S8G8I1 |
| C | Prolyl-tRNA synthetase (prors) (EC 6.1.1.15) | protein | 477 | 35% helix, 30% strand | S8G8I1 |
| D | Prolyl-tRNA synthetase (prors) (EC 6.1.1.15) | protein | 475 | 37% helix, 29% strand | S8G8I1 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
- 9SF · 3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 706 | 0.83 | 0.87 | 68 | empty |
| 2 | 919 | 0.82 | 0.84 | 80 | empty |
| 3 | 718 | 0.76 | 0.81 | 57 | ANP, MG, 9SF |
| 4 | 676 | 0.76 | 0.81 | 54 | ANP, MG, 9SF |
| 5 | 666 | 0.75 | 0.81 | 55 | ANP, MG, 9SF |
Interfaces
5 interfaces between chains.
- C–D · 2676 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 2676 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 403 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 341 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 12 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6A88 · Crystal Structure of T. gondii prolyl tRNA synthetase with Febrifugine and ATP Analog · the same entry in another collection · chain B against B, TM-score 1.00
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 S8G8I1
- Elsewhere: RCSB PDB 6A88 · PDBe 6A88 · UniProt S8G8I1
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