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Structure of rat nogo receptor bound to 1D9 antagonist antibody
Analyse Structure of rat nogo receptor bound to 1D9 antagonist antibody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KJ4
- Type
- protein
- Length
- 1,439 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab fragment 1D9 light chain; Fab fragment 1D9 heavy chain; Reticulon-4 receptor
- UniProt
- Q99M75
- Ligands
- NDG, NAG, MAN, ZN
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, B | Fab fragment 1D9 light chain | protein | 219 | 5% helix, 45% strand | — |
| H | Fab fragment 1D9 heavy chain | protein | 219 | 4% helix, 45% strand | — |
| A, D | Reticulon-4 receptor | protein | 283 | 6% helix, 16% strand | Q99M75 |
| C | Fab fragment 1D9 heavy chain | protein | 216 | 3% helix, 43% strand | — |
Ligands and binding sites
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 4 copies · chains A, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, D
- MAN · alpha-D-mannopyranose · sugar
- ZN · Zinc ion · metal · 2 copies · chains L, H, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 444 | 0.76 | 0.85 | 39 | ZN |
| 2 | 254 | 0.70 | 0.85 | 39 | ZN |
| 3 | 562 | 0.61 | 0.74 | 65 | empty |
| 4 | 312 | 0.60 | 0.78 | 37 | empty |
| 5 | 542 | 0.60 | 0.74 | 52 | empty |
Interfaces
6 interfaces between chains.
- L–H · 1875 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1853 Ų buried · 13 hydrogen bonds · protein-protein
- H–A · 597 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 534 Ų buried · 6 hydrogen bonds · protein-protein
- L–A · 293 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide (disulfide).
Compared structures
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 Q99M75
- Elsewhere: RCSB PDB 3KJ4 · PDBe 3KJ4 · UniProt Q99M75
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