MolNFT v1 · #148914 · protein
Drosophila plexin a in complex with semaphorin 1B
6FKM · Plexin a, isoform a: “Drosophila plexin a in complex with semaphorin 1B”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 11 pockets (best druggability 0.82). MolNFT v1 #148914 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6FKM
- Type
- protein
- Length
- 1,022 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plexin a, isoform a; MIP07328P
- UniProt
- Q9V491, Q7KK54
- Ligands
- NAG, MAN, BMA
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Plexin a, isoform a | protein | 512 | 9% helix, 41% strand | Q9V491 |
| B | MIP07328P | protein | 510 | 10% helix, 40% strand | Q7KK54 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains B, A
- MAN · alpha-D-mannopyranose · sugar · 4 copies
- BMA · beta-D-mannopyranose · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 852 | 0.82 | 0.85 | 95 | empty |
| 2 | 950 | 0.76 | 0.78 | 77 | empty |
| 3 | 643 | 0.72 | 0.79 | 54 | empty |
| 4 | 174 | 0.65 | 0.85 | 33 | empty |
| 5 | 129 | 0.54 | 0.82 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 989 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 7 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 6FKM · Drosophila Plexin A in complex with Semaphorin 1b · 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 Q9V491
- Every structure of UniProt Q7KK54
- Elsewhere: RCSB PDB 6FKM · PDBe 6FKM · UniProt Q9V491 · UniProt Q7KK54
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