MolNFT v1 · #87080 · protein
Crystal structure of the rgmb-NEO1 complex form 1
4BQ6 · Neogenin: “Crystal structure of the rgmb-NEO1 complex form 1”. X-ray diffraction, 1 ligand (NAG), 6 pockets (best druggability 0.85). MolNFT v1 #87080 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4BQ6
- Type
- protein
- Length
- 738 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neogenin; Rgm domain family member B
- UniProt
- P97798, Q6NW40
- Ligands
- NAG
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 6% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Neogenin | protein | 205 | 1% helix, 49% strand | P97798 |
| C | Rgm domain family member B | protein | 15 | 0% helix, 47% strand | Q6NW40 |
| D | Rgm domain family member B | protein | 148 | 9% helix, 46% strand | Q6NW40 |
| E | Rgm domain family member B | protein | 16 | 0% helix, 44% strand | Q6NW40 |
| F | Rgm domain family member B | protein | 149 | 9% helix, 46% strand | Q6NW40 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 868 | 0.85 | 0.87 | 122 | empty |
| 2 | 177 | 0.68 | 0.87 | 25 | empty |
| 3 | 304 | 0.65 | 0.81 | 28 | empty |
| 4 | 99 | 0.50 | 0.82 | 19 | empty |
| 5 | 66 | 0.33 | 0.76 | 16 | empty |
Interfaces
7 interfaces between chains.
- B–F · 1240 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1234 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1129 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1110 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 468 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4BQ6 · Crystal structure of the RGMB-NEO1 complex form 1 · the same entry in another collection · chain F against F, TM-score 1.00
- Q6NW40 · AlphaFold monomer V2.0 prediction for rgm domain family member B (Q6NW40) · a predicted model of the same protein · chain D against A, TM-score 0.98
- P97798 · AlphaFold monomer V2.0 prediction for neogenin (P97798) · a predicted model of the same protein · chain A against A, TM-score 0.74
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 P97798
- Every structure of UniProt Q6NW40
- Elsewhere: RCSB PDB 4BQ6 · PDBe 4BQ6 · UniProt P97798 · UniProt Q6NW40
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.