Research workbench
Rhodopseudomonas palustris prolyl-tRNA synthetase in complex with proams
Analyse Rhodopseudomonas palustris prolyl-tRNA synthetase in complex with proams in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2I4M
- Type
- protein
- Length
- 1,321 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
- Q6N5P6
- Ligands
- PSD
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proline-tRNA ligase (EC 6.1.1.15) | protein | 439 | 35% helix, 29% strand | Q6N5P6 |
| B, C | Proline-tRNA ligase (EC 6.1.1.15) | protein | 441 | 34% helix, 29% strand | Q6N5P6 |
Ligands and binding sites
- PSD · 5'-O-[N-(prolyl)-sulfamoyl]adenosine · ligand · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1053 | 0.85 | 0.86 | 111 | PSD |
| 2 | 95 | 0.75 | 0.96 | 22 | empty |
| 3 | 1075 | 0.73 | 0.76 | 98 | empty |
| 4 | 649 | 0.70 | 0.78 | 70 | empty |
| 5 | 455 | 0.65 | 0.78 | 50 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2479 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 547 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 266 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2I4M · Rhodopseudomonas palustris prolyl-tRNA synthetase in complex with ProAMS · the same entry in another collection · chain A against A, TM-score 1.00
- Q6N5P6 · AlphaFold monomer V2.0 prediction for proline--tRNA ligase (Q6N5P6) · a predicted model of the same protein · chain B 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 Q6N5P6
- Elsewhere: RCSB PDB 2I4M · PDBe 2I4M · UniProt Q6N5P6
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