MolNFT v1 · #10793 · protein + RNA
Crystal structure of archaeosine tRNA-guanine transglycosylase complexed with lambda-form TRNA(VAL)
1J2B: “Crystal structure of archaeosine tRNA-guanine transglycosylase complexed with lambda-form TRNA(VAL)”. X-ray diffraction, 2 ligands (MG, ZN), 19 pockets (best druggability 0.82). MolNFT v1 #10793 on GenesisL1: 3D structure, binding…
- PDB
- 1J2B
- Type
- protein + RNA
- Length
- 1,300 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA(VAL); Archaeosine tRNA-guanine transglycosylase
- EC
- 2.4.2.29
- UniProt
- O58843
- Ligands
- MG, ZN
- Pockets
- 19 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | TRNA(VAL) | rna | 77 | — | — |
| D | TRNA(VAL) | rna | 71 | — | — |
| A, B | Archaeosine tRNA-guanine transglycosylase (EC 2.4.2.29) | protein | 576 | 41% helix, 22% strand | O58843 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains C, A, D, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1005 | 0.82 | 0.83 | 79 | MG |
| 2 | 1160 | 0.80 | 0.82 | 101 | MG |
| 3 | 55 | 0.71 | 0.98 | 28 | empty |
| 4 | 463 | 0.60 | 0.76 | 21 | empty |
| 5 | 425 | 0.59 | 0.76 | 23 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2231 Ų buried · 33 hydrogen bonds · protein-protein
- C–A · 1870 Ų buried · 33 hydrogen bonds · protein-nucleic
- D–B · 1868 Ų buried · 29 hydrogen bonds · protein-nucleic
- C–B · 1739 Ų buried · 39 hydrogen bonds · protein-nucleic
- D–A · 1666 Ų buried · 44 hydrogen bonds · protein-nucleic
Compared structures
- 1J2B · Crystal Structure Of Archaeosine tRNA-Guanine Transglycosylase Complexed With lambda-form… · the same entry in another collection · chain C against C, TM-score 1.00
- O58843 · AlphaFold monomer V2.0 prediction for tRNA-GUANINE(15) transglycosylase (O58843) · a predicted model of the same protein · chain A 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 O58843
- Elsewhere: RCSB PDB 1J2B · PDBe 1J2B · UniProt O58843
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