Research workbench
Crystal structure of the phd-doc complex
Analyse Crystal structure of the phd-doc complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K33
- Type
- protein
- Length
- 347 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Death on curing protein; Prevent host death protein; Polypeptide of unknown amino acids…
- UniProt
- Q06259, Q06253
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 5 distinct chains · 56% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Death on curing protein | protein | 124 | 66% helix, 2% strand | Q06259 |
| B | Prevent host death protein | protein | 67 | 49% helix, 16% strand | Q06253 |
| C | Prevent host death protein | protein | 73 | 62% helix, 21% strand | Q06253 |
| D | Prevent host death protein | protein | 71 | 42% helix, 17% strand | Q06253 |
| E | Polypeptide of unknown amino acids and source | protein | 12 | 50% helix, 0% strand | — |
Ligands and binding sites
- ACT · Acetate ion · additive · 2 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 243 | 0.69 | 0.85 | 54 | empty |
| 2 | 208 | 0.45 | 0.73 | 33 | empty |
| 3 | 162 | 0.41 | 0.74 | 35 | ACT |
Interfaces
5 interfaces between chains.
- A–C · 1088 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 985 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 619 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 133 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 45 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3K33 · Crystal structure of the Phd-Doc complex · 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 3K33 · PDBe 3K33 · UniProt Q06259 · UniProt Q06253
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