MolNFT v1 · #87082 · protein
Crystal structure of the rgmb-NEO1 complex form 3
4BQ8 · Neogenin: “Crystal structure of the rgmb-NEO1 complex form 3”. X-ray diffraction, 1 ligand (NAG), 3 pockets (best druggability 0.62). MolNFT v1 #87082 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4BQ8
- Type
- protein
- Length
- 370 residues
- Chains
- 3
- 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
- 3 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neogenin | protein | 195 | 2% helix, 52% strand | P97798 |
| B | Rgm domain family member B | protein | 14 | 0% helix, 50% strand | Q6NW40 |
| C | Rgm domain family member B | protein | 161 | 14% helix, 45% strand | Q6NW40 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 239 | 0.62 | 0.81 | 36 | empty |
| 2 | 69 | 0.38 | 0.78 | 16 | empty |
| 3 | 64 | 0.33 | 0.77 | 22 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1232 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1135 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4BQ8 · Crystal structure of the RGMB-NEO1 complex form 3 · the same entry in another collection · chain A against A, 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 C against A, TM-score 0.96
- P97798 · AlphaFold monomer V2.0 prediction for neogenin (P97798) · a predicted model of the same protein · chain A against A, TM-score 0.78
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 4BQ8 · PDBe 4BQ8 · UniProt P97798 · UniProt Q6NW40
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