Research workbench
Drosophila semaphorin 2B
Analyse Drosophila semaphorin 2B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QP8
- Type
- protein
- Length
- 1,242 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IP13724P
- UniProt
- Q29QV5
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | IP13724P | protein | 622 | 10% helix, 40% strand | Q29QV5 |
| B | IP13724P | protein | 620 | 11% helix, 41% strand | Q29QV5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 26 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 21 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- FLC · Citrate anion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 781 | 0.81 | 0.84 | 72 | NAG, MAN |
| 2 | 870 | 0.78 | 0.81 | 61 | empty |
| 3 | 796 | 0.76 | 0.80 | 55 | NAG |
| 4 | 68 | 0.67 | 0.94 | 23 | empty |
| 5 | 129 | 0.63 | 0.87 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1974 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide, 14 glycan (disulfide, N-glycosylation).
Compared structures
- 6QP8 · Drosophila Semaphorin 2b · the same entry in another collection · chain A against A, TM-score 1.00
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 Q29QV5
- Elsewhere: RCSB PDB 6QP8 · PDBe 6QP8 · UniProt Q29QV5
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