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Crystal structure of ORP8 pH domain in P1211 space group
Analyse Crystal structure of ORP8 pH domain in P1211 space group in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U78
- Type
- protein
- Length
- 479 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxysterol-binding protein-related protein 8
- UniProt
- Q9BZF1
- Pockets
- 8 · best druggability 0.51
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxysterol-binding protein-related protein 8 | protein | 120 | 15% helix, 37% strand | Q9BZF1 |
| B | Oxysterol-binding protein-related protein 8 | protein | 122 | 14% helix, 35% strand | Q9BZF1 |
| C | Oxysterol-binding protein-related protein 8 | protein | 116 | 16% helix, 37% strand | Q9BZF1 |
| D | Oxysterol-binding protein-related protein 8 | protein | 121 | 16% helix, 38% strand | Q9BZF1 |
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 258 | 0.51 | 0.75 | 22 | empty |
| 2 | 167 | 0.46 | 0.76 | 22 | empty |
| 3 | 180 | 0.44 | 0.74 | 22 | empty |
| 4 | 104 | 0.36 | 0.74 | 27 | empty |
| 5 | 84 | 0.33 | 0.73 | 16 | empty |
Interfaces
4 interfaces between chains.
- B–D · 457 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 431 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 103 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 89 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5U78 · Crystal structure of ORP8 PH domain in P1211 space group · the same entry in another collection · chain D against D, TM-score 1.00
- Q9BZF1 · AlphaFold monomer V2.0 prediction for oxysterol-binding protein- related protein 8… · a predicted model of the same protein · chain C against A, TM-score 0.95
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 Q9BZF1
- Elsewhere: RCSB PDB 5U78 · PDBe 5U78 · UniProt Q9BZF1
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