MolNFT v1 · #115217 · protein + RNA
Structure of an asymmetric tetramer of human tRNA M1A58 methyltransferase in a complex with sah and TRNA3LYS
5CD1 · TRNA (ADENINE(58)-N(1))-methyltransferase catalytic subunit…: “Structure of an asymmetric tetramer of human tRNA M1A58 methyltransferase in a complex with sah and TRNA3LYS”. X-ray diffraction, 2 ligands (SAH, NA), 20 pockets (best…
- PDB
- 5CD1
- Type
- protein + RNA
- Length
- 1,400 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (ADENINE(58)-N(1))-methyltransferase catalytic subunit TRMT61A; TRNA…
- EC
- 2.1.1.220
- UniProt
- Q96FX7, Q9UJA5
- Ligands
- SAH, NA
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | TRNA (ADENINE(58)-N(1))-methyltransferase catalytic subunit TRMT61A (EC 2.1.1.220) | protein | 281 | 27% helix, 29% strand | Q96FX7 |
| B | TRNA (ADENINE(58)-N(1))-methyltransferase non-catalytic subunit TRM6 | protein | 321 | 36% helix, 26% strand | Q9UJA5 |
| E | TRNA (ADENINE(58)-N(1))-methyltransferase non-catalytic subunit TRM6 | protein | 367 | 36% helix, 25% strand | Q9UJA5 |
| M | TRNA3LYS | rna | 74 | — | — |
| N | TRNA3LYS | rna | 76 | — | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, E, M, D, N
- NA · Sodium ion · metal · 2 copies · chains M, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 331 | 0.81 | 0.92 | 54 | empty |
| 2 | 510 | 0.78 | 0.86 | 75 | empty |
| 3 | 495 | 0.78 | 0.86 | 63 | SAH |
| 4 | 434 | 0.75 | 0.84 | 55 | empty |
| 5 | 62 | 0.74 | 0.98 | 18 | empty |
Interfaces
12 interfaces between chains.
- D–E · 2611 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 2513 Ų buried · 34 hydrogen bonds · protein-protein
- E–M · 1694 Ų buried · 41 hydrogen bonds · protein-nucleic
- A–E · 1664 Ų buried · 28 hydrogen bonds · protein-protein
- D–N · 1437 Ų buried · 26 hydrogen bonds · protein-nucleic
Compared structures
- 5CD1 · Structure of an asymmetric tetramer of human tRNA m1A58 methyltransferase in a complex… · the same entry in another collection · chain N against N, TM-score 1.00
- Q9UJA5 · AlphaFold monomer V2.0 prediction for tRNA (ADENINE(58)-N(1))-methyltransferase… · a predicted model of the same protein · chain B against A, TM-score 0.97
- Q96FX7 · AlphaFold monomer V2.0 prediction for tRNA (ADENINE(58)-N(1))-methyltransferase catalytic… · a predicted model of the same protein · chain D against A, TM-score 0.97
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 Q96FX7
- Every structure of UniProt Q9UJA5
- Elsewhere: RCSB PDB 5CD1 · PDBe 5CD1 · UniProt Q96FX7 · UniProt Q9UJA5
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