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Crystal structure of a rigid four spectrin repeat fragment of the human desmoplakin plakin domain
Analyse Crystal structure of a rigid four spectrin repeat fragment of the human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R6N
- Type
- protein
- Length
- 897 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Desmoplakin
- UniProt
- P15924
- Ligands
- D1D
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 71% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Desmoplakin | protein | 450 | 71% helix, 6% strand | P15924 |
| B | Desmoplakin | protein | 447 | 71% helix, 6% strand | P15924 |
Ligands and binding sites
- D1D · (4S,5S)-1,2-dithiane-4,5-diol · ligand · 2 copies · chains A, B
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 956 | 0.71 | 0.75 | 72 | empty |
| 2 | 77 | 0.40 | 0.78 | 14 | D1D |
| 3 | 51 | 0.35 | 0.79 | 9 | D1D |
| 4 | 56 | 0.30 | 0.75 | 15 | empty |
| 5 | 51 | 0.25 | 0.72 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 260 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3R6N · Crystal structure of a rigid four spectrin repeat fragment of the human desmoplakin… · the same entry in another collection · chain A against A, TM-score 1.00
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 P15924
- Elsewhere: RCSB PDB 3R6N · PDBe 3R6N · UniProt P15924
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