MolNFT v1 · #153668 · protein
Structure of scgn in complex with a SNAP25 peptide
6JLH · Secretagogin: “Structure of scgn in complex with a SNAP25 peptide”. X-ray diffraction, 2 ligands (CA, CL), 7 pockets (best druggability 0.85). MolNFT v1 #153668 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6JLH
- Type
- protein
- Length
- 551 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Secretagogin; Synaptosomal-associated protein 25
- UniProt
- Q5XJX1, P60880
- Ligands
- CA, CL
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 60% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Secretagogin | protein | 261 | 60% helix, 3% strand | Q5XJX1 |
| B, D | Synaptosomal-associated protein 25 | protein | 17 | 82% helix, 0% strand | P60880 |
| C | Secretagogin | protein | 256 | 59% helix, 3% strand | Q5XJX1 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1117 | 0.85 | 0.86 | 104 | empty |
| 2 | 596 | 0.81 | 0.86 | 49 | empty |
| 3 | 106 | 0.44 | 0.78 | 23 | CL |
| 4 | 66 | 0.38 | 0.79 | 16 | empty |
| 5 | 58 | 0.33 | 0.76 | 12 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1500 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 909 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 909 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 112 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 105 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 6JLH · Structure of SCGN in complex with a Snap25 peptide · the same entry in another collection · chain B against B, TM-score 1.00
- P60880 · AlphaFold monomer V2.0 prediction for synaptosomal-associated protein 25 (P60880) · a predicted model of the same protein · chain B against A, TM-score 0.70
- Q5XJX1 · AlphaFold monomer V2.0 prediction for secretagogin (Q5XJX1) · 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 Q5XJX1
- Every structure of UniProt P60880
- Elsewhere: RCSB PDB 6JLH · PDBe 6JLH · UniProt Q5XJX1 · UniProt P60880
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