Research workbench
Crystal structure of ORP1-ord in complex with PI(4,5)P2
Analyse Crystal structure of ORP1-ord in complex with PI(4,5)P2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZM6
- Type
- protein
- Length
- 764 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxysterol-binding protein-related protein 1
- UniProt
- Q9BXW6
- Ligands
- IEP
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxysterol-binding protein-related protein 1 | protein | 392 | 29% helix, 31% strand | Q9BXW6 |
| B | Oxysterol-binding protein-related protein 1 | protein | 372 | 28% helix, 33% strand | Q9BXW6 |
Ligands and binding sites
- IEP · [(2~{S})-1-octadecanoyloxy-3-[oxidanyl-[(1~{R},2~{R}, 3~{S},4~{S},5~{S},6~{S})-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] icosa-5,8,11,14-tetraenoate · ligand · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 910 | 0.79 | 0.81 | 72 | IEP |
| 2 | 455 | 0.73 | 0.83 | 56 | IEP |
| 3 | 173 | 0.51 | 0.78 | 22 | empty |
| 4 | 280 | 0.49 | 0.73 | 39 | empty |
| 5 | 101 | 0.40 | 0.76 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 644 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5ZM6 · Crystal structure of ORP1-ORD in complex with PI(4,5)P2 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BXW6 · AlphaFold monomer V2.0 prediction for oxysterol-binding protein- related protein 1… · a predicted model of the same protein · chain B 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 Q9BXW6
- Elsewhere: RCSB PDB 5ZM6 · PDBe 5ZM6 · UniProt Q9BXW6
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