MolNFT v1 · #58213 · protein
Bifunctional tRNA modification enzyme mnmc from escherichia COLI
3AWI · TRNA 5-methylaminomethyl-2-thiouridine biosynthesis…: “Bifunctional tRNA modification enzyme mnmc from escherichia COLI”. X-ray diffraction, 2 ligands (FAD, SO4), 20 pockets (best druggability 0.86). MolNFT v1 #58213 on GenesisL1…
- PDB
- 3AWI
- Type
- protein
- Length
- 3,799 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein mnmc
- EC
- 2.1.1.61, 1.5.-.-
- UniProt
- P77182
- Ligands
- FAD, SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F | TRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein mnmc (EC 2.1.1.61, 1.5.-.-) | protein | 628 | 35% helix, 25% strand | P77182 |
| D | TRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein mnmc (EC 2.1.1.61, 1.5.-.-) | protein | 659 | 33% helix, 23% strand | P77182 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 11 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 914 | 0.86 | 0.87 | 123 | FAD, SO4 |
| 2 | 528 | 0.82 | 0.88 | 83 | FAD |
| 3 | 841 | 0.81 | 0.84 | 97 | FAD, SO4 |
| 4 | 788 | 0.81 | 0.84 | 89 | FAD, SO4 |
| 5 | 758 | 0.80 | 0.84 | 87 | FAD, SO4 |
Interfaces
5 interfaces between chains.
- C–F · 1353 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 1119 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 895 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 866 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 599 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3AWI · Bifunctional tRNA modification enzyme MnmC from Escherichia coli · the same entry in another collection · chain F against F, TM-score 1.00
- P77182 · AlphaFold monomer V2.0 prediction for tRNA 5-methylaminomethyl-2-thiouridine biosynthesis… · a predicted model of the same protein · chain A against A, TM-score 1.00
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 P77182
- Elsewhere: RCSB PDB 3AWI · PDBe 3AWI · UniProt P77182
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