Research workbench
Crystal structure of the mammalian MDC1 fha domain complexed with CHK2 PTHR68 peptide
Analyse Crystal structure of the mammalian MDC1 fha domain complexed with CHK2 PTHR68… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VA4
- Type
- protein
- Length
- 227 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mediator of DNA damage checkpoint protein 1; SERINE/THREONINE-protein kinase CHK2
- UniProt
- Q5PSV9, O96017
- Pockets
- 2 · best druggability 0.46
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mediator of DNA damage checkpoint protein 1 | protein | 111 | 0% helix, 43% strand | Q5PSV9 |
| C | SERINE/THREONINE-protein kinase CHK2 | protein | 8 | 0% helix, 0% strand | O96017 |
| B | Mediator of DNA damage checkpoint protein 1 | protein | 108 | 0% helix, 44% strand | Q5PSV9 |
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 | 102 | 0.46 | 0.79 | 17 | empty |
| 2 | 77 | 0.37 | 0.77 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–B · 694 Ų buried · 9 hydrogen bonds · protein-protein
- C–B · 346 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 3VA4 · Crystal structure of the mammalian MDC1 FHA domain complexed with CHK2 pThr68 peptide · the same entry in another collection · chain A against A, TM-score 1.00
- Q5PSV9 · AlphaFold monomer V2.0 prediction for mediator of DNA damage checkpoint protein 1 (Q5PSV9) · a predicted model of the same protein · chain B against A, TM-score 0.97
- O96017 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase CHK2 (O96017) · a predicted model of the same protein · chain C against A, TM-score 0.50
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 Q5PSV9
- Every structure of UniProt O96017
- Elsewhere: RCSB PDB 3VA4 · PDBe 3VA4 · UniProt Q5PSV9 · UniProt O96017
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