Research workbench
Molecular mechanism of guidance cue recognition
Analyse Molecular mechanism of guidance cue recognition in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NVQ
- Type
- protein
- Length
- 2,124 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Semaphorin-7A; Plexin-C1
- UniProt
- O75326, O60486
- Ligands
- NAG, NDG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Semaphorin-7A | protein | 588 | 5% helix, 39% strand | O75326 |
| B, F | Plexin-C1 | protein | 474 | 6% helix, 38% strand | O60486 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 21 copies · chains A, B, E, F
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1075 | 0.81 | 0.82 | 83 | empty |
| 2 | 1176 | 0.80 | 0.82 | 91 | empty |
| 3 | 323 | 0.77 | 0.89 | 54 | empty |
| 4 | 958 | 0.72 | 0.76 | 52 | empty |
| 5 | 1005 | 0.71 | 0.75 | 56 | empty |
Interfaces
3 interfaces between chains.
- A–E · 1561 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1148 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 1108 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 34 disulfide, 22 glycan (disulfide, N-glycosylation).
Compared structures
- 3NVQ · Molecular mechanism of guidance cue recognition · the same entry in another collection · chain A against A, TM-score 1.00
- O75326 · AlphaFold monomer V2.0 prediction for semaphorin-7A (O75326) · a predicted model of the same protein · chain A against A, TM-score 1.00
- O60486 · AlphaFold monomer V2.0 prediction for plexin-C1 (O60486) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 O75326
- Every structure of UniProt O60486
- Elsewhere: RCSB PDB 3NVQ · PDBe 3NVQ · UniProt O75326 · UniProt O60486
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