MolNFT v1 · #104872 · protein
Crystal structure of cmob bound with cx-SAM in P21212
4QNU · TRNA (MO5U34)-methyltransferase: “Crystal structure of cmob bound with cx-SAM in P21212”. X-ray diffraction, 2 ligands (GEK, PO4), 20 pockets (best druggability 0.69). MolNFT v1 #104872 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4QNU
- Type
- protein
- Length
- 2,571 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (MO5U34)-methyltransferase
- EC
- 2.1.1.-
- UniProt
- A1AC32
- Ligands
- GEK, PO4
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, F, G | TRNA (MO5U34)-methyltransferase (EC 2.1.1.-) | protein | 323 | 34% helix, 27% strand | A1AC32 |
| B, C, H | TRNA (MO5U34)-methyltransferase (EC 2.1.1.-) | protein | 320 | 33% helix, 27% strand | A1AC32 |
| E | TRNA (MO5U34)-methyltransferase (EC 2.1.1.-) | protein | 319 | 33% helix, 27% strand | A1AC32 |
Ligands and binding sites
- GEK · (2S)-4-[{[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}(carboxylatomethyl)sulfonio] -2-ammoniobutanoate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- PO4 · Phosphate ion · ion · 10 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 403 | 0.69 | 0.81 | 43 | GEK |
| 2 | 435 | 0.68 | 0.80 | 42 | GEK |
| 3 | 390 | 0.68 | 0.81 | 46 | GEK |
| 4 | 412 | 0.68 | 0.80 | 47 | GEK |
| 5 | 387 | 0.67 | 0.80 | 40 | GEK |
Interfaces
9 interfaces between chains.
- E–H · 967 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 949 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 942 Ų buried · 13 hydrogen bonds · protein-protein
- F–G · 908 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 543 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
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 A1AC32
- Elsewhere: RCSB PDB 4QNU · PDBe 4QNU · UniProt A1AC32
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