MolNFT v1 · #167855 · protein
Cryo-EM structure of the full-length A39R/PLEXINC1 complex
6VXK · Semaphorin-like protein 139: “Cryo-EM structure of the full-length A39R/PLEXINC1 complex”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.82). MolNFT v1 #167855 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6VXK
- Type
- protein
- Length
- 2,254 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Semaphorin-like protein 139; Plexin-C1
- UniProt
- Q8JL80, O60486
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 2 distinct chains · 4% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Semaphorin-like protein 139 | protein | 380 | 6% helix, 45% strand | Q8JL80 |
| B, D | Plexin-C1 | protein | 747 | 4% helix, 42% strand | O60486 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, B, C, D
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 | 931 | 0.82 | 0.83 | 74 | empty |
| 2 | 943 | 0.80 | 0.82 | 72 | empty |
| 3 | 608 | 0.72 | 0.80 | 46 | empty |
| 4 | 591 | 0.71 | 0.79 | 40 | empty |
| 5 | 491 | 0.69 | 0.80 | 41 | empty |
Interfaces
3 interfaces between chains.
- C–D · 973 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 967 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 903 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 34 disulfide, 18 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 6VXK · PDBe 6VXK · UniProt Q8JL80 · UniProt O60486
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