Research workbench
Crystal structure of the full-length tRNA isopentenylpyrophosphate transferase (BH2366) from bacillus halodurans, northeast structural genomics consortium target BHR41.
Analyse Crystal structure of the full-length tRNA isopentenylpyrophosphate transferase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EXA
- Type
- protein
- Length
- 1,210 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA DELTA(2)-isopentenylpyrophosphate transferase
- EC
- 2.5.1.8
- UniProt
- Q9KAC3
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | TRNA DELTA(2)-isopentenylpyrophosphate transferase (EC 2.5.1.8) | protein | 303 | 56% helix, 11% strand | Q9KAC3 |
| B, D | TRNA DELTA(2)-isopentenylpyrophosphate transferase (EC 2.5.1.8) | protein | 302 | 55% helix, 11% strand | Q9KAC3 |
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 739 | 0.78 | 0.83 | 76 | empty |
| 2 | 615 | 0.78 | 0.84 | 69 | empty |
| 3 | 721 | 0.78 | 0.82 | 71 | empty |
| 4 | 564 | 0.78 | 0.84 | 64 | empty |
| 5 | 461 | 0.66 | 0.78 | 53 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1705 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1697 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 209 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 205 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 modified (engineered).
Compared structures
- 3EXA · Crystal structure of the full-length tRNA isopentenylpyrophosphate transferase (BH2366)… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KAC3 · AlphaFold monomer V2.0 prediction for tRNA dimethylallyltransferase (Q9KAC3) · a predicted model of the same protein · chain B against A, TM-score 0.81
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 Q9KAC3
- Elsewhere: RCSB PDB 3EXA · PDBe 3EXA · UniProt Q9KAC3
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