MolNFT v1 · #82026 · protein
Crystal structure of the mammalian MDC1 fha domain
3VA1 · Mediator of DNA damage checkpoint protein 1: “Crystal structure of the mammalian MDC1 fha domain”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.40). MolNFT v1 #82026 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3VA1
- Type
- protein
- Length
- 214 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mediator of DNA damage checkpoint protein 1
- UniProt
- Q5PSV9
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.40
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mediator of DNA damage checkpoint protein 1 | protein | 107 | 0% helix, 46% strand | Q5PSV9 |
| B | Mediator of DNA damage checkpoint protein 1 | protein | 107 | 0% helix, 44% strand | Q5PSV9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
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 | 60 | 0.40 | 0.81 | 19 | empty |
| 2 | 67 | 0.40 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 786 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3VA1 · Crystal structure of the mammalian MDC1 FHA domain · 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 0.98
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 Q5PSV9
- Elsewhere: RCSB PDB 3VA1 · PDBe 3VA1 · UniProt Q5PSV9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.