Research workbench
Crystal structure of arabidopsis glutamyl-tRNA reductase in complex with its binding protein
Analyse Crystal structure of arabidopsis glutamyl-tRNA reductase in complex with its… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4N7R
- Type
- protein
- Length
- 1,293 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamyl-tRNA reductase 1, chloroplastic; Genomic DNA, chromosome 3, P1 clone: MXL8
- EC
- 1.2.1.70
- UniProt
- P42804, Q9LU39
- Pockets
- 15 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamyl-tRNA reductase 1, chloroplastic (EC 1.2.1.70) | protein | 405 | 54% helix, 16% strand | P42804 |
| C | Genomic DNA, chromosome 3, P1 clone: MXL8 | protein | 252 | 29% helix, 33% strand | Q9LU39 |
| B | Glutamyl-tRNA reductase 1, chloroplastic (EC 1.2.1.70) | protein | 385 | 51% helix, 14% strand | P42804 |
| D | Genomic DNA, chromosome 3, P1 clone: MXL8 | protein | 251 | 30% helix, 32% strand | Q9LU39 |
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 | 1173 | 0.75 | 0.78 | 118 | empty |
| 2 | 357 | 0.73 | 0.84 | 37 | empty |
| 3 | 440 | 0.69 | 0.80 | 43 | empty |
| 4 | 139 | 0.68 | 0.89 | 33 | empty |
| 5 | 699 | 0.68 | 0.76 | 80 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1698 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1177 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 664 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 649 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4N7R · Crystal structure of Arabidopsis glutamyl-tRNA reductase in complex with its binding… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9LU39 · AlphaFold monomer V2.0 prediction for glutamyl-tRNA reductase-binding protein… · a predicted model of the same protein · chain C against A, TM-score 0.99
- P42804 · AlphaFold monomer V2.0 prediction for glutamyl-tRNA reductase 1, chloroplastic (P42804) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 4N7R · PDBe 4N7R · UniProt P42804 · UniProt Q9LU39
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