MolNFT v1 · #61156 · protein
Structure of DOCH66Y in complex with the C-terminal domain of phd
3DD7 · Death on curing protein: “Structure of DOCH66Y in complex with the C-terminal domain of phd”. X-ray diffraction, 1 ligand (BR), 2 pockets (best druggability 0.57). MolNFT v1 #61156 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3DD7
- Type
- protein
- Length
- 285 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Death on curing protein; Prevent host death protein
- UniProt
- Q06259, Q06253
- Ligands
- BR
- Pockets
- 2 · best druggability 0.57
Structure
x-ray diffraction · 4 distinct chains · 68% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Death on curing protein | protein | 123 | 66% helix, 2% strand | Q06259 |
| B | Prevent host death protein | protein | 18 | 83% helix, 0% strand | Q06253 |
| C | Death on curing protein | protein | 122 | 66% helix, 0% strand | Q06259 |
| D | Prevent host death protein | protein | 22 | 77% helix, 0% strand | Q06253 |
Ligands and binding sites
- BR · Bromide ion · ion · 16 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 257 | 0.57 | 0.78 | 33 | BR |
| 2 | 133 | 0.39 | 0.74 | 24 | BR |
Interfaces
4 interfaces between chains.
- C–D · 1035 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 900 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 286 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 64 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (engineered).
Compared structures
- 3DD7 · Structure of DocH66Y in complex with the C-terminal domain of Phd · 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 Q06259
- Every structure of UniProt Q06253
- Elsewhere: RCSB PDB 3DD7 · PDBe 3DD7 · UniProt Q06259 · UniProt Q06253
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