MolNFT v1 · #160579 · protein
Crystal structure of the human NELL1 EGF1-3-ROBO3 FN1 complex
6POL · Roundabout homolog 3: “Crystal structure of the human NELL1 EGF1-3-ROBO3 FN1 complex”. X-ray diffraction, 3 ligands (NAG, CA, NO3), 7 pockets (best druggability 0.71). MolNFT v1 #160579 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6POL
- Type
- protein
- Length
- 690 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Roundabout homolog 3; Protein kinase C-binding protein NELL1
- UniProt
- Q96MS0, Q92832
- Ligands
- NAG, CA, NO3
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 1% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Roundabout homolog 3 | protein | 102 | 0% helix, 40% strand | Q96MS0 |
| B, D, F | Protein kinase C-binding protein NELL1 | protein | 129 | 2% helix, 40% strand | Q92832 |
| C | Roundabout homolog 3 | protein | 101 | 0% helix, 41% strand | Q96MS0 |
| E | Roundabout homolog 3 | protein | 100 | 0% helix, 41% strand | Q96MS0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains B, D, F
- CA · Calcium ion · metal · 3 copies · chains B, D, F
- NO3 · Nitrate ion · ion · 14 copies · chains A, B, F, C, D, E
- GOL · Glycerol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 903 | 0.71 | 0.75 | 64 | NO3 |
| 2 | 300 | 0.53 | 0.75 | 39 | NO3 |
| 3 | 122 | 0.45 | 0.77 | 26 | NO3 |
| 4 | 149 | 0.43 | 0.74 | 23 | empty |
| 5 | 106 | 0.42 | 0.77 | 22 | empty |
Interfaces
7 interfaces between chains.
- E–F · 930 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 920 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 920 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 350 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 261 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6POL · Crystal structure of the human NELL1 EGF1-3-Robo3 FN1 complex · the same entry in another collection · chain F against F, TM-score 1.00
- Q96MS0 · AlphaFold monomer V2.0 prediction for roundabout homolog 3 (Q96MS0) · a predicted model of the same protein · chain E against A, TM-score 0.95
- Q92832 · AlphaFold monomer V2.0 prediction for protein kinase C-binding protein NELL1 (Q92832) · a predicted model of the same protein · chain B against A, TM-score 0.58
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 Q92832
- Elsewhere: RCSB PDB 6POL · PDBe 6POL · UniProt Q96MS0 · UniProt Q92832
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