Research workbench
Structure of cyclodipeptide synthase from candidatus glomeribacter gigasporarum bound to phe-trnaphe
Analyse Structure of cyclodipeptide synthase from candidatus glomeribacter gigasporarum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y4B
- Type
- protein + RNA
- Length
- 331 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (77-mer); Cyclodipeptide synthase
- UniProt
- G2JBB2
- Ligands
- PHE
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | RNA (77-mer) | rna | 76 | — | — |
| A | Cyclodipeptide synthase | protein | 255 | 47% helix, 4% strand | G2JBB2 |
Ligands and binding sites
- PHE · Phenylalanine · ligand · chains F, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 955 | 0.79 | 0.81 | 86 | empty |
| 2 | 1138 | 0.79 | 0.81 | 110 | PHE |
| 3 | 439 | 0.63 | 0.78 | 27 | empty |
| 4 | 114 | 0.51 | 0.81 | 24 | empty |
| 5 | 311 | 0.48 | 0.73 | 23 | empty |
Interfaces
1 interface between chains.
- F–A · 334 Ų buried · 0 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 7 modified, 1 covalent (nucleotide modification, covalent ligand).
Compared structures
- 6Y4B · Structure of cyclodipeptide synthase from Candidatus Glomeribacter gigasporarum bound to… · the same entry in another collection · chain F against F, 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 G2JBB2
- Elsewhere: RCSB PDB 6Y4B · PDBe 6Y4B · UniProt G2JBB2
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