Research workbench
Crystal structure of the yeast mitochondrial holliday junction resolvase, YDC2
Analyse Crystal structure of the yeast mitochondrial holliday junction resolvase, YDC2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KCF
- Type
- protein
- Length
- 468 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical 30.2 kd protein C25G10.02 in chromosome I
- EC
- 3.1.-.-
- UniProt
- Q10423
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical 30.2 kd protein C25G10.02 in chromosome I (EC 3.1.-.-) | protein | 240 | 51% helix, 15% strand | Q10423 |
| B | Hypothetical 30.2 kd protein C25G10.02 in chromosome I (EC 3.1.-.-) | protein | 228 | 51% helix, 15% strand | Q10423 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 255 | 0.54 | 0.76 | 39 | empty |
| 2 | 130 | 0.41 | 0.75 | 25 | empty |
| 3 | 96 | 0.40 | 0.77 | 15 | empty |
| 4 | 130 | 0.40 | 0.74 | 21 | empty |
| 5 | 91 | 0.36 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 760 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1KCF · Crystal Structure of the Yeast Mitochondrial Holliday Junction Resolvase, Ydc2 · the same entry in another collection · chain A against A, TM-score 1.00
- Q10423 · AlphaFold monomer V2.0 prediction for cruciform cutting endonuclease 1, mitochondrial… · a predicted model of the same protein · chain B 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 Q10423
- Elsewhere: RCSB PDB 1KCF · PDBe 1KCF · UniProt Q10423
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