MolNFT v1 · #154855 · protein
Crystal structure of SNX11-pxe domain in complex with PI(3,5)P2
6KOJ · Sorting nexin-11: “Crystal structure of SNX11-pxe domain in complex with PI(3,5)P2”. X-ray diffraction, 1 ligand (I35), 1 pocket (best druggability 0.63). MolNFT v1 #154855 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6KOJ
- Type
- protein
- Length
- 255 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sorting nexin-11
- UniProt
- Q9Y5W9
- Ligands
- I35
- Pockets
- 1 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sorting nexin-11 | protein | 127 | 43% helix, 22% strand | Q9Y5W9 |
| B | Sorting nexin-11 | protein | 128 | 43% helix, 22% strand | Q9Y5W9 |
Ligands and binding sites
- I35 · [(2~{R})-2-butanoyloxy-3-[oxidanyl-[(2~{R},3~{R},5~{S}, 6~{R})-2,4,6-tris(oxidanyl)-3,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] butanoate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 618 | 0.63 | 0.74 | 48 | I35 |
Interfaces
1 interface between chains.
- A–B · 411 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
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 Q9Y5W9
- Elsewhere: RCSB PDB 6KOJ · PDBe 6KOJ · UniProt Q9Y5W9
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