MolNFT v1 · #181637 · protein
Cryo-EM structure of the SEMA3A/PLEXINA4/NEUROPILIN 1 complex
7M0R · Neuropilin-1: “Cryo-EM structure of the SEMA3A/PLEXINA4/NEUROPILIN 1 complex”. Electron microscopy, 1 ligand (CA), 20 pockets (best druggability 0.84). MolNFT v1 #181637 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7M0R
- Type
- protein
- Length
- 4,358 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuropilin-1; Semaphorin-3A; Plexin-A4
- UniProt
- P97333, O08665, Q80UG2
- Ligands
- CA
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 6% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, F | Neuropilin-1 | protein | 458 | 2% helix, 48% strand | P97333 |
| C, D | Semaphorin-3A | protein | 588 | 9% helix, 40% strand | O08665 |
| A, B | Plexin-A4 | protein | 1133 | 6% helix, 39% strand | Q80UG2 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains E, B, F, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1006 | 0.84 | 0.85 | 87 | empty |
| 2 | 697 | 0.82 | 0.86 | 54 | empty |
| 3 | 683 | 0.82 | 0.86 | 64 | empty |
| 4 | 1103 | 0.80 | 0.82 | 129 | empty |
| 5 | 1151 | 0.80 | 0.82 | 130 | empty |
Interfaces
7 interfaces between chains.
- C–D · 1331 Ų buried · 17 hydrogen bonds · protein-protein
- D–B · 1275 Ų buried · 13 hydrogen bonds · protein-protein
- C–A · 1209 Ų buried · 12 hydrogen bonds · protein-protein
- E–C · 1000 Ų buried · 5 hydrogen bonds · protein-protein
- F–D · 945 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 70 disulfide (disulfide).
Compared structures
- 7M0R · Cryo-EM structure of the Sema3A/PlexinA4/Neuropilin 1 complex · the same entry in another collection · chain B against B, TM-score 1.00
- O08665 · AlphaFold monomer V2.0 prediction for semaphorin-3A (O08665) · a predicted model of the same protein · chain C against A, TM-score 0.98
- P97333 · AlphaFold monomer V2.0 prediction for neuropilin-1 (P97333) · a predicted model of the same protein · chain E against A, TM-score 0.74
- Q80UG2 · AlphaFold monomer V2.0 prediction for plexin-A4 (Q80UG2) · a predicted model of the same protein · chain A against A, TM-score 0.64
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 P97333
- Every structure of UniProt O08665
- Every structure of UniProt Q80UG2
- Elsewhere: RCSB PDB 7M0R · PDBe 7M0R · UniProt P97333 · UniProt O08665 · UniProt Q80UG2
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