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Crystal structure of T. gondii prolyl tRNA synthetase with febrifugine and ATP analog
Analyse Crystal structure of T. gondii prolyl tRNA synthetase with febrifugine and ATP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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