Research workbench
Crystal structure of phd truncated to residue 57 in an orthorhombic space group
Analyse Crystal structure of phd truncated to residue 57 in an orthorhombic space group in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HS2
- Type
- protein
- Length
- 442 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prevent host death protein
- UniProt
- Q06253
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 6 distinct chains · 52% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Prevent host death protein | protein | 56 | 54% helix, 23% strand | Q06253 |
| C | Prevent host death protein | protein | 58 | 50% helix, 22% strand | Q06253 |
| E | Prevent host death protein | protein | 54 | 50% helix, 24% strand | Q06253 |
| F | Prevent host death protein | protein | 55 | 55% helix, 22% strand | Q06253 |
| G | Prevent host death protein | protein | 52 | 50% helix, 25% strand | Q06253 |
| H | Prevent host death protein | protein | 55 | 51% helix, 24% strand | Q06253 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains B, C, D, F, G, H
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 | 306 | 0.55 | 0.76 | 43 | empty |
| 2 | 112 | 0.38 | 0.74 | 22 | empty |
Interfaces
16 interfaces between chains.
- G–H · 1421 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1417 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1398 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 1338 Ų buried · 21 hydrogen bonds · protein-protein
- F–G · 366 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3HS2 · Crystal structure of PHD truncated to residue 57 in an orthorhombic space group · 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 Q06253
- Elsewhere: RCSB PDB 3HS2 · PDBe 3HS2 · UniProt Q06253
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