Research workbench
Crystal structure of K. lactis Ddc2 N-terminus in complex with S. cerevisiae Rfa1 (K45E mutant) N-OB domain
Analyse Crystal structure of K. lactis Ddc2 N-terminus in complex with S. cerevisiae… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OMC
- Type
- protein
- Length
- 435 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.38
- Source
- Kluyveromyces lactis; Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
- Molecule
- Replication factor A protein 1; DNA damage checkpoint protein LCD1
- UniProt
- P22336, Q6CUV9
- Ligands
- CL
- Pockets
- 2 · best druggability 0.34
Structure
x-ray diffraction · resolution 2.38 · 3 distinct chains · 40% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Replication factor A protein 1 | protein | 121 | 23% helix, 37% strand | P22336 |
| B | Replication factor A protein 1 | protein | 120 | 29% helix, 36% strand | P22336 |
| C, D | DNA damage checkpoint protein LCD1 | protein | 97 | 73% helix, 0% strand | Q6CUV9 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.34 | 0.75 | 16 | CL |
| 2 | 70 | 0.31 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1994 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 877 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 861 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5OMC · Crystal structure of K. lactis DDC2 N-terminus in complex with S. cerevisiae RFA1 (K45E… · the same entry in another collection · chain A against A, TM-score 1.00
- P22336 · AlphaFold monomer V2.0 prediction for replication factor a protein 1 (P22336) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q6CUV9 · AlphaFold monomer V2.0 prediction for DNA damage checkpoint protein LCD1 (Q6CUV9) · a predicted model of the same protein · chain C against A, TM-score 0.74
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 P22336
- Every structure of UniProt Q6CUV9
- Elsewhere: RCSB PDB 5OMC · PDBe 5OMC · UniProt P22336 · UniProt Q6CUV9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.