MolNFT v1 · #140717 · protein
Crystal structure of arabidopsis glutamyl-tRNA reductase in complex with NADPH and gbp
5YJL · Glutamyl-tRNA reductase 1: “Crystal structure of arabidopsis glutamyl-tRNA reductase in complex with NADPH and gbp”. X-ray diffraction, 1 ligand (NAP), 15 pockets (best druggability 0.70). MolNFT v1 #140717 on GenesisL1: 3D…
- PDB
- 5YJL
- Type
- protein
- Length
- 1,330 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamyl-tRNA reductase 1; Glutamyl-tRNA reductase-binding protein
- EC
- 1.2.1.70
- UniProt
- P42804, Q9LU39
- Ligands
- NAP
- Pockets
- 15 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamyl-tRNA reductase 1 (EC 1.2.1.70) | protein | 411 | 56% helix, 14% strand | P42804 |
| C | Glutamyl-tRNA reductase-binding protein | protein | 251 | 29% helix, 33% strand | Q9LU39 |
| B | Glutamyl-tRNA reductase 1 (EC 1.2.1.70) | protein | 415 | 58% helix, 15% strand | P42804 |
| D | Glutamyl-tRNA reductase-binding protein | protein | 253 | 29% helix, 30% strand | Q9LU39 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 489 | 0.70 | 0.80 | 45 | NAP |
| 2 | 142 | 0.67 | 0.88 | 27 | empty |
| 3 | 177 | 0.67 | 0.86 | 32 | empty |
| 4 | 484 | 0.66 | 0.78 | 62 | empty |
| 5 | 410 | 0.64 | 0.78 | 44 | NAP |
Interfaces
4 interfaces between chains.
- C–D · 1668 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1584 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 707 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 675 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5YJL · Crystal structure of Arabidopsis glutamyl-tRNA reductase in complex with NADPH and GBP · the same entry in another collection · chain C against C, TM-score 1.00
- Q9LU39 · AlphaFold monomer V2.0 prediction for glutamyl-tRNA reductase-binding protein… · a predicted model of the same protein · chain D against A, TM-score 1.00
- P42804 · AlphaFold monomer V2.0 prediction for glutamyl-tRNA reductase 1, chloroplastic (P42804) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P42804
- Every structure of UniProt Q9LU39
- Elsewhere: RCSB PDB 5YJL · PDBe 5YJL · UniProt P42804 · UniProt Q9LU39
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