Research workbench
Crystal structure of IGLON5/NEGR1 heterodimer
Analyse Crystal structure of IGLON5/NEGR1 heterodimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DLD
- Type
- protein
- Length
- 1,056 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iglon family member 5; Neuronal growth regulator 1
- UniProt
- A6NGN9, Q7Z3B1
- Ligands
- NAG, BMA, MAN
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 2% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Iglon family member 5 | protein | 273 | 3% helix, 60% strand | A6NGN9 |
| B | Neuronal growth regulator 1 | protein | 247 | 1% helix, 50% strand | Q7Z3B1 |
| C | Iglon family member 5 | protein | 267 | 2% helix, 57% strand | A6NGN9 |
| D | Neuronal growth regulator 1 | protein | 269 | 2% helix, 50% strand | Q7Z3B1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 17 copies · chains A, D, B, C
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1190 | 0.81 | 0.82 | 112 | NAG |
| 2 | 85 | 0.66 | 0.91 | 21 | empty |
| 3 | 111 | 0.56 | 0.84 | 23 | empty |
| 4 | 149 | 0.54 | 0.81 | 31 | empty |
| 5 | 84 | 0.45 | 0.81 | 23 | NAG |
Interfaces
5 interfaces between chains.
- C–D · 800 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 791 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 619 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 436 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 129 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 glycan, 12 disulfide (N-glycosylation, disulfide).
Compared structures
- 6DLD · Crystal structure of IgLON5/NEGR1 heterodimer · the same entry in another collection · chain D against D, TM-score 1.00
- Q7Z3B1 · AlphaFold monomer V2.0 prediction for neuronal growth regulator 1 (Q7Z3B1) · a predicted model of the same protein · chain B against A, TM-score 0.93
- A6NGN9 · AlphaFold monomer V2.0 prediction for iglon family member 5 (A6NGN9) · a predicted model of the same protein · chain C against A, TM-score 0.86
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 A6NGN9
- Every structure of UniProt Q7Z3B1
- Elsewhere: RCSB PDB 6DLD · PDBe 6DLD · UniProt A6NGN9 · UniProt Q7Z3B1
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