MolNFT v1 · #185747 · protein
Crystal structure of prolyl-tRNA synthetase (prors, proline-tRNA ligase) from plasmodium falciparum in complex with MAT436
7QC1 · Proline--tRNA ligase: “Crystal structure of prolyl-tRNA synthetase (prors, proline-tRNA ligase) from plasmodium falciparum in…”. X-ray diffraction, 1 ligand (9XM), 17 pockets (best druggability 0.77). MolNFT v1 #185747 on GenesisL1…
- PDB
- 7QC1
- Type
- protein
- Length
- 1,455 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proline--tRNA ligase
- EC
- 6.1.1.15
- UniProt
- Q8I5R7
- Ligands
- 9XM
- Pockets
- 17 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proline--tRNA ligase (EC 6.1.1.15) | protein | 488 | 36% helix, 29% strand | Q8I5R7 |
| D | Proline--tRNA ligase (EC 6.1.1.15) | protein | 489 | 36% helix, 29% strand | Q8I5R7 |
| I | Proline--tRNA ligase (EC 6.1.1.15) | protein | 478 | 35% helix, 29% strand | Q8I5R7 |
Ligands and binding sites
- 9XM · [(2~{R},3~{S})-2-[3-(7-bromanyl-6-chloranyl-4-oxidanylidene-quinazolin-3-yl)-2-oxidanylidene-propyl]piperidin-3-yl] ~{N}-[4-[[3-(2,3-dihydro-1~{H}-inden-2-ylcarbamoyl)pyrazin-2-yl]carbamoyl]piperazin-1-yl]sulfonylcarbamate · ligand · 3 copies · chains A, D, I
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, I, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 940 | 0.77 | 0.79 | 81 | EDO |
| 2 | 840 | 0.74 | 0.78 | 88 | 9XM |
| 3 | 683 | 0.71 | 0.78 | 57 | EDO |
| 4 | 649 | 0.71 | 0.78 | 55 | 9XM, EDO |
| 5 | 589 | 0.71 | 0.79 | 58 | 9XM, EDO |
Interfaces
2 interfaces between chains.
- A–I · 2579 Ų buried · 37 hydrogen bonds · protein-protein
- A–D · 704 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7QC1 · Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline-tRNA ligase) from Plasmodium… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8I5R7 · AlphaFold monomer V2.0 prediction for proline--tRNA ligase (Q8I5R7) · a predicted model of the same protein · chain I against A, 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 Q8I5R7
- Elsewhere: RCSB PDB 7QC1 · PDBe 7QC1 · UniProt Q8I5R7
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