MolNFT v1 · #93332 · protein
Complex of mouse plexin A2 - semaphorin 3A - neuropilin-1
4GZA · Plexin-A2: “Complex of mouse plexin A2 - semaphorin 3A - neuropilin-1”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.82). MolNFT v1 #93332 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4GZA
- Type
- protein
- Length
- 4,537 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plexin-A2; Semaphorin-3A; Neuropilin-1
- UniProt
- P70207, O08665, P97333
- Ligands
- CA
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Plexin-A2 | protein | 656 | 11% helix, 39% strand | P70207 |
| G | Semaphorin-3A | protein | 484 | 8% helix, 39% strand | O08665 |
| H | Neuropilin-1 | protein | 117 | 3% helix, 42% strand | P97333 |
Ligands and binding sites
- CA · Calcium ion · metal · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1178 | 0.82 | 0.83 | 96 | empty |
| 2 | 932 | 0.78 | 0.80 | 100 | empty |
| 3 | 934 | 0.77 | 0.80 | 95 | empty |
| 4 | 903 | 0.77 | 0.80 | 93 | empty |
| 5 | 1148 | 0.77 | 0.79 | 125 | empty |
Interfaces
15 interfaces between chains.
- A–G · 1231 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1228 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1116 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1093 Ų buried · 11 hydrogen bonds · protein-protein
- A–H · 460 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 90 disulfide (disulfide).
Compared structures
- 4GZA · Complex of mouse Plexin A2 - Semaphorin 3A - Neuropilin-1 · the same entry in another collection · chain H against H, TM-score 1.00
- O08665 · AlphaFold monomer V2.0 prediction for semaphorin-3A (O08665) · a predicted model of the same protein · chain G against A, TM-score 0.99
- P97333 · AlphaFold monomer V2.0 prediction for neuropilin-1 (P97333) · a predicted model of the same protein · chain H against A, TM-score 0.99
- P70207 · AlphaFold monomer V2.0 prediction for plexin-A2 (P70207) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P70207
- Every structure of UniProt O08665
- Every structure of UniProt P97333
- Elsewhere: RCSB PDB 4GZA · PDBe 4GZA · UniProt P70207 · UniProt O08665 · UniProt P97333
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