Research workbench
Crystal structure of the NELL2 EGF1-6-ROBO3 FN1 complex
Analyse Crystal structure of the NELL2 EGF1-6-ROBO3 FN1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6POG
- Type
- protein
- Length
- 337 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Roundabout homolog 3; Protein kinase C-binding protein NELL2
- UniProt
- Q96MS0, Q99435
- Ligands
- NAG, FUC, CA
- Pockets
- 4 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 1% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Roundabout homolog 3 | protein | 101 | 0% helix, 44% strand | Q96MS0 |
| B | Protein kinase C-binding protein NELL2 | protein | 236 | 2% helix, 39% strand | Q99435 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains B
- FUC · alpha-L-fucopyranose · sugar
- CA · Calcium ion · metal · 3 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.47 | 0.75 | 25 | empty |
| 2 | 97 | 0.42 | 0.78 | 24 | empty |
| 3 | 57 | 0.31 | 0.76 | 15 | empty |
| 4 | 61 | 0.27 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 957 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 2 glycan (disulfide, N-glycosylation, O-glycosylation).
Compared structures
- 6POG · Crystal structure of the NELL2 EGF1-6-Robo3 FN1 complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q96MS0 · AlphaFold monomer V2.0 prediction for roundabout homolog 3 (Q96MS0) · a predicted model of the same protein · chain A against A, TM-score 0.93
- Q99435 · AlphaFold monomer V2.0 prediction for protein kinase C-binding protein NELL2 (Q99435) · a predicted model of the same protein · chain B against A, TM-score 0.44
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 Q96MS0
- Every structure of UniProt Q99435
- Elsewhere: RCSB PDB 6POG · PDBe 6POG · UniProt Q96MS0 · UniProt Q99435
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