MolNFT v1 · #141881 · protein
Crystal structure of ORP2-ord in complex with PI(4,5)P2
5ZM8 · Oxysterol-binding protein-related protein 2: “Crystal structure of ORP2-ord in complex with PI(4,5)P2”. X-ray diffraction, 1 ligand (IEP), 10 pockets (best druggability 0.75). MolNFT v1 #141881 on GenesisL1: 3D structure, binding…
- PDB
- 5ZM8
- Type
- protein
- Length
- 799 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxysterol-binding protein-related protein 2
- UniProt
- Q9H1P3
- Ligands
- IEP
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxysterol-binding protein-related protein 2 | protein | 386 | 26% helix, 32% strand | Q9H1P3 |
| B | Oxysterol-binding protein-related protein 2 | protein | 413 | 27% helix, 30% strand | Q9H1P3 |
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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 532 | 0.75 | 0.82 | 59 | IEP |
| 2 | 352 | 0.75 | 0.85 | 39 | empty |
| 3 | 354 | 0.60 | 0.77 | 46 | empty |
| 4 | 185 | 0.59 | 0.81 | 22 | empty |
| 5 | 138 | 0.55 | 0.82 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 631 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5ZM8 · Crystal structure of ORP2-ORD in complex with PI(4,5)P2 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H1P3 · AlphaFold monomer V2.0 prediction for oxysterol-binding protein- related protein 2… · a predicted model of the same protein · chain B against A, TM-score 0.92
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 Q9H1P3
- Elsewhere: RCSB PDB 5ZM8 · PDBe 5ZM8 · UniProt Q9H1P3
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