Research workbench
Crystal structure of the rgmb-NEO1 complex form 2
Analyse Crystal structure of the rgmb-NEO1 complex form 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BQ7
- Type
- protein
- Length
- 730 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
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Neogenin | protein | 202 | 1% helix, 50% strand | P97798 |
| C, E | Rgm domain family member B | protein | 15 | 0% helix, 47% strand | Q6NW40 |
| D, F | Rgm domain family member B | protein | 148 | 9% helix, 46% strand | Q6NW40 |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 476 | 0.71 | 0.81 | 52 | empty |
| 2 | 302 | 0.70 | 0.84 | 58 | empty |
| 3 | 210 | 0.63 | 0.83 | 35 | empty |
| 4 | 67 | 0.37 | 0.78 | 17 | empty |
| 5 | 59 | 0.31 | 0.76 | 16 | empty |
Interfaces
7 interfaces between chains.
- A–D · 1206 Ų buried · 17 hydrogen bonds · protein-protein
- B–F · 1183 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1115 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 1113 Ų buried · 21 hydrogen bonds · protein-protein
- A–F · 276 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4BQ7 · Crystal structure of the RGMB-Neo1 complex form 2 · 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 0.77
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 4BQ7 · PDBe 4BQ7 · UniProt P97798 · UniProt Q6NW40
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