MolNFT v1 · #161790 · protein
Drosophila semaphorin 1A, extracellular domains 1-2
6QP9 · Semaphorin-1A: “Drosophila semaphorin 1A, extracellular domains 1-2”. X-ray diffraction, 1 ligand (NAG), 19 pockets (best druggability 0.78). MolNFT v1 #161790 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6QP9
- Type
- protein
- Length
- 1,009 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Semaphorin-1A
- UniProt
- Q24322
- Ligands
- NAG
- Pockets
- 19 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Semaphorin-1A | protein | 505 | 6% helix, 32% strand | Q24322 |
| B | Semaphorin-1A | protein | 504 | 7% helix, 31% strand | Q24322 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1083 | 0.78 | 0.80 | 108 | empty |
| 2 | 689 | 0.77 | 0.82 | 63 | NAG |
| 3 | 755 | 0.77 | 0.81 | 72 | empty |
| 4 | 56 | 0.63 | 0.93 | 19 | empty |
| 5 | 75 | 0.59 | 0.89 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 782 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 4 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 Q24322
- Elsewhere: RCSB PDB 6QP9 · PDBe 6QP9 · UniProt Q24322
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