MolNFT v1 · #30851 · protein
Crystal structure of aquaporin Z tetramer reveals both open and closed water-conducting channels
2ABM: “Crystal structure of aquaporin Z tetramer reveals both open and closed water-conducting channels”. X-ray diffraction, 6 ligands (PEE, BGL, 3PG), 20 pockets (best druggability 0.88). MolNFT v1 #30851 on GenesisL1: 3D structure…
- PDB
- 2ABM
- Type
- protein
- Length
- 1,816 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aquaporin Z
- UniProt
- P60844
- Ligands
- PEE, BGL, 3PG, AGA, POQ, PO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Aquaporin Z | protein | 227 | 72% helix, 0% strand | P60844 |
Ligands and binding sites
- PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · 7 copies · chains A, C, B, D, F, E, G, H
- BGL · 2-O-octyl-beta-D-glucopyranose · ligand · 4 copies · chains A, E, B, F
- 3PG · 3-phosphoglyceric acid · ligand · 2 copies · chains C, G
- AGA · (1S)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(pentanoyloxy)methyl]ethyl octanoate · ligand · 2 copies · chains C, G
- POQ · Bis(((3s,4s,5r,6r)-5-(ethyl(phosphoryloxy))-3,4,6-trihydroxy-tetrahydro-2H-pyran-2-yl)methyl) hydrogen phosphate · ligand · chains A, B, E, F
- PO4 · Phosphate ion · ion · 4 copies · chains B, C, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1175 | 0.88 | 0.89 | 84 | BGL, POQ |
| 2 | 916 | 0.84 | 0.85 | 83 | PEE |
| 3 | 900 | 0.83 | 0.85 | 81 | PEE |
| 4 | 185 | 0.55 | 0.79 | 41 | empty |
| 5 | 248 | 0.54 | 0.76 | 34 | empty |
Interfaces
16 interfaces between chains.
- G–H · 1678 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 1674 Ų buried · 6 hydrogen bonds · protein-protein
- E–G · 1672 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 1671 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 1663 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2ABM · Crystal Structure of Aquaporin Z Tetramer Reveals both Open and Closed Water-conducting… · the same entry in another collection · chain H against H, TM-score 1.00
- P60844 · AlphaFold monomer V2.0 prediction for aquaporin Z (P60844) · a predicted model of the same protein · chain F 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 P60844
- Elsewhere: RCSB PDB 2ABM · PDBe 2ABM · UniProt P60844
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