MolNFT v1 · #158599 · protein
Cryo-EM structure of aav-2 in complex with aavr pkd domains 1 and 2
6NZ0 · Dyslexia-associated protein KIAA0319-like protein: “Cryo-EM structure of aav-2 in complex with aavr pkd domains 1 and 2”. Electron microscopy, 1 ligand (MG), 5 pockets (best druggability 0.71). MolNFT v1 #158599 on GenesisL1: 3D…
- PDB
- 6NZ0
- Type
- protein
- Length
- 594 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dyslexia-associated protein KIAA0319-like protein; Capsid protein VP1
- UniProt
- Q8IZA0, P03135
- Ligands
- MG
- Pockets
- 5 · best druggability 0.71
Structure
electron microscopy · 2 distinct chains · 6% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Z | Dyslexia-associated protein KIAA0319-like protein | protein | 95 | 0% helix, 47% strand | Q8IZA0 |
| A | Capsid protein VP1 | protein | 499 | 7% helix, 36% strand | P03135 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains Z
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 958 | 0.71 | 0.76 | 103 | empty |
| 2 | 109 | 0.44 | 0.78 | 16 | empty |
| 3 | 82 | 0.42 | 0.79 | 19 | empty |
| 4 | 131 | 0.40 | 0.74 | 21 | empty |
| 5 | 91 | 0.33 | 0.73 | 23 | empty |
Interfaces
1 interface between chains.
- Z–A · 573 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6NZ0 · Cryo-EM structure of AAV-2 in complex with AAVR PKD domains 1 and 2 · the same entry in another collection · chain Z against Z, TM-score 1.00
- Q8IZA0 · AlphaFold monomer V2.0 prediction for dyslexia-associated protein KIAA0319-like protein… · a predicted model of the same protein · chain Z against A, TM-score 0.97
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 Q8IZA0
- Every structure of UniProt P03135
- Elsewhere: RCSB PDB 6NZ0 · PDBe 6NZ0 · UniProt Q8IZA0 · UniProt P03135
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