MolNFT v1 · #63944 · protein + RNA
Structure of E. COLI isopentenyl-tRNA transferase in complex with E. COLI TRNA(PHE)
3FOZ · TRNA DELTA(2)-isopentenylpyrophosphate transferase: “Structure of E. COLI isopentenyl-tRNA transferase in complex with E. COLI TRNA(PHE)”. X-ray diffraction, 1 ligand (CA), 13 pockets (best druggability 0.67). MolNFT v1 #63944 on…
- PDB
- 3FOZ
- Type
- protein + RNA
- Length
- 751 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA DELTA(2)-isopentenylpyrophosphate transferase; TRNA(PHE)
- EC
- 2.5.1.8
- UniProt
- P16384
- Ligands
- CA
- Pockets
- 13 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA DELTA(2)-isopentenylpyrophosphate transferase (EC 2.5.1.8) | protein | 305 | 53% helix, 11% strand | P16384 |
| B | TRNA DELTA(2)-isopentenylpyrophosphate transferase (EC 2.5.1.8) | protein | 303 | 52% helix, 11% strand | P16384 |
| C | TRNA(PHE) | rna | 74 | — | — |
| D | TRNA(PHE) | rna | 69 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 22 copies · chains B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 222 | 0.67 | 0.85 | 37 | empty |
| 2 | 589 | 0.64 | 0.76 | 34 | CA |
| 3 | 490 | 0.63 | 0.77 | 33 | CA |
| 4 | 469 | 0.61 | 0.76 | 44 | CA |
| 5 | 426 | 0.61 | 0.77 | 25 | CA |
Interfaces
4 interfaces between chains.
- B–D · 2126 Ų buried · 55 hydrogen bonds · protein-nucleic
- A–C · 2060 Ų buried · 52 hydrogen bonds · protein-nucleic
- A–B · 401 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 263 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 3FOZ · Structure of E. coli Isopentenyl-tRNA transferase in complex with E. coli tRNA(Phe) · the same entry in another collection · chain A against A, TM-score 1.00
- P16384 · AlphaFold monomer V2.0 prediction for tRNA dimethylallyltransferase (P16384) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P16384
- Elsewhere: RCSB PDB 3FOZ · PDBe 3FOZ · UniProt P16384
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