Research workbench
Crystal structure of MJKAE1-PFUPCC1 complex
Analyse Crystal structure of MJKAE1-PFUPCC1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JMV
- Type
- protein
- Length
- 1,325 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein…
- EC
- 2.3.1.234, 2.7.11.1
- UniProt
- Q58530, Q8TZI1
- Ligands
- AMP, MG
- Pockets
- 14 · best druggability 0.72
Structure
x-ray diffraction · 8 distinct chains · 48% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein (EC 2.3.1.234, 2.7.11.1) | protein | 323 | 48% helix, 20% strand | Q58530 |
| B | Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein (EC 2.3.1.234, 2.7.11.1) | protein | 321 | 48% helix, 20% strand | Q58530 |
| C | Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein (EC 2.3.1.234, 2.7.11.1) | protein | 318 | 48% helix, 20% strand | Q58530 |
| D | Uncharacterized protein | protein | 78 | 47% helix, 29% strand | Q8TZI1 |
| E | Uncharacterized protein | protein | 72 | 49% helix, 32% strand | Q8TZI1 |
| F | Uncharacterized protein | protein | 76 | 47% helix, 30% strand | Q8TZI1 |
| G | Uncharacterized protein | protein | 72 | 49% helix, 32% strand | Q8TZI1 |
| H | Uncharacterized protein | protein | 65 | 52% helix, 23% strand | Q8TZI1 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 752 | 0.72 | 0.78 | 89 | AMP |
| 2 | 432 | 0.66 | 0.79 | 49 | AMP |
| 3 | 268 | 0.65 | 0.82 | 20 | empty |
| 4 | 387 | 0.64 | 0.79 | 44 | AMP |
| 5 | 251 | 0.63 | 0.81 | 41 | empty |
Interfaces
11 interfaces between chains.
- A–D · 969 Ų buried · 9 hydrogen bonds · protein-protein
- B–F · 913 Ų buried · 10 hydrogen bonds · protein-protein
- F–G · 864 Ų buried · 12 hydrogen bonds · protein-protein
- C–H · 863 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 829 Ų buried · 12 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 Q58530
- Every structure of UniProt Q8TZI1
- Elsewhere: RCSB PDB 5JMV · PDBe 5JMV · UniProt Q58530 · UniProt Q8TZI1
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