MolNFT v1 · #82029 · protein
Crystal structure of the mammalian MDC1 fha domain complexed with CHK2 PTHR68 peptide
3VA4 · Mediator of DNA damage checkpoint protein 1: “Crystal structure of the mammalian MDC1 fha domain complexed with CHK2 PTHR68 peptide”. X-ray diffraction, 2 pockets (best druggability 0.46). MolNFT v1 #82029 on GenesisL1: 3D…
- 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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