Research workbench
Crystal structure of the zig-8-rig-5 IG1-IG1 heterodimer, tetragonal form
Analyse Crystal structure of the zig-8-rig-5 IG1-IG1 heterodimer, tetragonal form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ON9
- Type
- protein
- Length
- 226 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zwei ig domain protein zig-8; Neuronal igcam-5
- UniProt
- G5ED00, C6KRM7
- Ligands
- NAG, FUC, NA, SO4
- Pockets
- 2 · best druggability 0.42
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Zwei ig domain protein zig-8 | protein | 116 | 9% helix, 45% strand | G5ED00 |
| B | Neuronal igcam-5 | protein | 110 | 3% helix, 52% strand | C6KRM7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
- FUC · alpha-L-fucopyranose · sugar · chains B
- NA · Sodium ion · metal · chains B
- SO4 · Sulfate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.42 | 0.82 | 21 | empty |
| 2 | 61 | 0.29 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1007 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6ON9 · Crystal Structure of the ZIG-8-RIG-5 IG1-IG1 heterodimer, tetragonal form · the same entry in another collection · chain A against A, TM-score 1.00
- G5ED00 · AlphaFold monomer V2.0 prediction for zwei ig domain protein zig-8 (G5ED00) · a predicted model of the same protein · chain A 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 G5ED00
- Every structure of UniProt C6KRM7
- Elsewhere: RCSB PDB 6ON9 · PDBe 6ON9 · UniProt G5ED00 · UniProt C6KRM7
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