Research workbench
Crystal structure of MDC1 fha domain in complex with a phosphorylated peptide from the MDC1 N-terminus
Analyse Crystal structure of MDC1 fha domain in complex with a phosphorylated peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UOT
- Type
- protein
- Length
- 240 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mediator of DNA damage checkpoint protein 1
- UniProt
- Q14676
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 2% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mediator of DNA damage checkpoint protein 1 | protein | 117 | 3% helix, 42% strand | Q14676 |
| B | Mediator of DNA damage checkpoint protein 1 | protein | 107 | 0% helix, 44% strand | Q14676 |
| D, E | Mediator of DNA damage checkpoint protein 1 | protein | 8 | 0% helix, 0% strand | Q14676 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 171 | 0.63 | 0.84 | 23 | empty |
| 2 | 114 | 0.46 | 0.78 | 22 | empty |
| 3 | 51 | 0.39 | 0.81 | 13 | empty |
Interfaces
5 interfaces between chains.
- A–B · 487 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 399 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 391 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 102 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 93 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered, phosphorylation).
Compared structures
- 3UOT · Crystal Structure of MDC1 FHA Domain in Complex with a Phosphorylated Peptide from the… · the same entry in another collection · chain E against E, TM-score 1.00
- Q14676 · AlphaFold monomer V2.0 prediction for mediator of DNA damage checkpoint protein 1 (Q14676) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q14676
- Elsewhere: RCSB PDB 3UOT · PDBe 3UOT · UniProt Q14676
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