Research workbench
Structure of E. COLI 5-methyluridine methyltransferase trma in complex with 19 nucleotide T-arm analogue
Analyse Structure of E. COLI 5-methyluridine methyltransferase trma in complex with 19… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BT7
- Type
- protein + RNA
- Length
- 776 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (uracil-5-)-methyltransferase; RNA (5'-D(P*GP*CP*UP*GP*UP*GP*(5MU)…
- EC
- 2.1.1.35
- UniProt
- P23003
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | TRNA (uracil-5-)-methyltransferase (EC 2.1.1.35) | protein | 369 | 33% helix, 29% strand | P23003 |
| C, D | RNA (5'-D(P*GP*CP*UP*GP*UP*GP*(5MU) P*UP*CP*GP*AP*UP*CP*CP*AP*CP*AP*GP*C)-3') | rna | 19 | — | — |
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 657 | 0.76 | 0.82 | 63 | empty |
| 2 | 725 | 0.75 | 0.80 | 63 | empty |
| 3 | 240 | 0.48 | 0.75 | 31 | empty |
| 4 | 76 | 0.41 | 0.78 | 14 | empty |
| 5 | 75 | 0.39 | 0.78 | 14 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1142 Ų buried · 37 hydrogen bonds · protein-nucleic
- A–C · 1137 Ų buried · 42 hydrogen bonds · protein-nucleic
- C–D · 219 Ų buried · 6 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3BT7 · Structure of E. coli 5-Methyluridine Methyltransferase TrmA in complex with 19 nucleotide… · the same entry in another collection · chain A against A, TM-score 1.00
- P23003 · AlphaFold monomer V2.0 prediction for TRNA/TMRNA (uracil-C(5))-methyltransferase (P23003) · a predicted model of the same protein · chain A 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 P23003
- Elsewhere: RCSB PDB 3BT7 · PDBe 3BT7 · UniProt P23003
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