MolNFT v1 · #74040 · protein
Receptor-ligand structure of human semaphorin 4D with plexin B1.
3OL2 · Semaphorin-4D: “Receptor-ligand structure of human semaphorin 4D with plexin B1.”. X-ray diffraction, 2 ligands (NAG, BMA), 13 pockets (best druggability 0.81). MolNFT v1 #74040 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3OL2
- Type
- protein
- Length
- 1,110 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Semaphorin-4D; Plexin-B1
- UniProt
- Q92854, O43157
- Ligands
- NAG, BMA
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Semaphorin-4D | protein | 614 | 10% helix, 42% strand | Q92854 |
| B | Plexin-B1 | protein | 496 | 10% helix, 39% strand | O43157 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 3 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 938 | 0.81 | 0.83 | 108 | empty |
| 2 | 1016 | 0.79 | 0.81 | 82 | empty |
| 3 | 940 | 0.74 | 0.78 | 76 | empty |
| 4 | 387 | 0.64 | 0.79 | 50 | empty |
| 5 | 156 | 0.57 | 0.82 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1330 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 3OL2 · Receptor-ligand structure of Human Semaphorin 4D with Plexin B1. · the same entry in another collection · chain A against A, TM-score 1.00
- Q92854 · AlphaFold monomer V2.0 prediction for semaphorin-4D (Q92854) · a predicted model of the same protein · chain A against A, TM-score 1.00
- O43157 · AlphaFold monomer V2.0 prediction for plexin-B1 (O43157) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q92854
- Every structure of UniProt O43157
- Elsewhere: RCSB PDB 3OL2 · PDBe 3OL2 · UniProt Q92854 · UniProt O43157
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