MolNFT v1 · #114226 · protein + RNA
Crystal structures of E.COLI arginyl-tRNA synthetase (argrs) in complex with substrate TRNA(ARG)
5B63 · Arginine--tRNA ligase: “Crystal structures of E.COLI arginyl-tRNA synthetase (argrs) in complex with substrate TRNA(ARG)”. X-ray diffraction, 20 pockets (best druggability 0.84). MolNFT v1 #114226 on GenesisL1: 3D structure, binding…
- PDB
- 5B63
- Type
- protein + RNA
- Length
- 1,243 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginine--tRNA ligase; TRNA-arg
- EC
- 6.1.1.19
- UniProt
- P11875
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arginine--tRNA ligase (EC 6.1.1.19) | protein | 563 | 49% helix, 9% strand | P11875 |
| B | TRNA-arg | rna | 63 | — | — |
| C | Arginine--tRNA ligase (EC 6.1.1.19) | protein | 553 | 44% helix, 10% strand | P11875 |
| D | TRNA-arg | rna | 64 | — | — |
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1184 | 0.84 | 0.85 | 105 | empty |
| 2 | 1057 | 0.81 | 0.83 | 85 | empty |
| 3 | 1127 | 0.77 | 0.80 | 66 | empty |
| 4 | 625 | 0.72 | 0.79 | 58 | empty |
| 5 | 464 | 0.71 | 0.81 | 48 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1744 Ų buried · 35 hydrogen bonds · protein-nucleic
- C–D · 1528 Ų buried · 28 hydrogen bonds · protein-nucleic
- A–C · 1113 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 54 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 5B63 · Crystal structures of E.coli arginyl-tRNA synthetase (ArgRS) in complex with substrate… · the same entry in another collection · chain A against A, TM-score 1.00
- P11875 · AlphaFold monomer V2.0 prediction for arginine--tRNA ligase (P11875) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P11875
- Elsewhere: RCSB PDB 5B63 · PDBe 5B63 · UniProt P11875
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