Research workbench
Crystal structure of K. lactis DDC2 N-terminus in complex with S. cerevisiae RFA1 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
- 5OMB
- Type
- protein
- Length
- 448 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replication factor a protein 1; DNA damage checkpoint protein LCD1
- UniProt
- P22336, Q6CUV9
- Ligands
- CL
- Pockets
- 3 · best druggability 0.41
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Replication factor a protein 1 | protein | 124 | 27% helix, 36% strand | P22336 |
| B | Replication factor a protein 1 | protein | 128 | 26% helix, 35% strand | P22336 |
| C, D | DNA damage checkpoint protein LCD1 | protein | 98 | 73% helix, 0% strand | Q6CUV9 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 96 | 0.41 | 0.77 | 18 | EDO |
| 2 | 84 | 0.39 | 0.77 | 22 | empty |
| 3 | 56 | 0.28 | 0.74 | 12 | CL |
Interfaces
3 interfaces between chains.
- C–D · 2018 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 987 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 982 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 5OMB · Crystal structure of K. lactis Ddc2 N-terminus in complex with S. cerevisiae Rfa1 N-OB… · 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 0.97
- 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 0.75
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 5OMB · PDBe 5OMB · UniProt P22336 · UniProt Q6CUV9
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