MolNFT v1 · #148915 · protein
Drosophila plexin a in complex with semaphorin 1B
6FKN · Plexin a, isoform a: “Drosophila plexin a in complex with semaphorin 1B”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.86). MolNFT v1 #148915 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6FKN
- Type
- protein
- Length
- 1,974 residues
- Chains
- 4
- 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
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Plexin a, isoform a | protein | 511 | 9% helix, 41% strand | Q9V491 |
| B | MIP07328P | protein | 478 | 11% helix, 41% strand | Q7KK54 |
| C | Plexin a, isoform a | protein | 512 | 9% helix, 41% strand | Q9V491 |
| D | MIP07328P | protein | 473 | 11% helix, 42% strand | Q7KK54 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains B, D, A, C
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains C
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 933 | 0.86 | 0.88 | 116 | empty |
| 2 | 1066 | 0.82 | 0.83 | 104 | empty |
| 3 | 551 | 0.77 | 0.84 | 49 | empty |
| 4 | 588 | 0.75 | 0.82 | 59 | empty |
| 5 | 635 | 0.72 | 0.80 | 52 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1062 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 995 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 524 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 498 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 23 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 6FKN · 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 6FKN · PDBe 6FKN · UniProt Q9V491 · UniProt Q7KK54
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