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
- 3NVN
- Type
- protein
- Length
- 857 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- EVM139; Plexin-C1
- UniProt
- Q8JL80, O60486
- Ligands
- NAG, NDG, CA
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | EVM139 | protein | 383 | 5% helix, 44% strand | Q8JL80 |
| B | Plexin-C1 | protein | 474 | 6% helix, 38% strand | O60486 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains B
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 3 copies · chains A, B
- CA · Calcium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1093 | 0.81 | 0.82 | 81 | empty |
| 2 | 667 | 0.73 | 0.80 | 51 | empty |
| 3 | 397 | 0.60 | 0.76 | 32 | empty |
| 4 | 226 | 0.54 | 0.78 | 31 | empty |
| 5 | 157 | 0.48 | 0.78 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 1044 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 8 glycan (disulfide, N-glycosylation).
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 Q8JL80
- Every structure of UniProt O60486
- Elsewhere: RCSB PDB 3NVN · PDBe 3NVN · UniProt Q8JL80 · UniProt O60486
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