MolNFT v1 · #102242 · protein
Crystal structure of the complex of syg-1 D1-D2 and syg-2 D1-D4
4OFY · Protein syg-1, isoform B: “Crystal structure of the complex of syg-1 D1-D2 and syg-2 D1-D4”. X-ray diffraction, 2 ligands (EMC, NAG), 6 pockets (best druggability 0.56). MolNFT v1 #102242 on GenesisL1: 3D structure, binding sites…
- PDB
- 4OFY
- Type
- protein
- Length
- 1,905 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein syg-1, isoform B; Protein syg-2
- UniProt
- B1Q236, Q9U3P2
- Ligands
- EMC, NAG
- Pockets
- 6 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein syg-1, isoform B | protein | 230 | 4% helix, 47% strand | B1Q236 |
| B, C | Protein syg-1, isoform B | protein | 227 | 4% helix, 46% strand | B1Q236 |
| D, E, F | Protein syg-2 | protein | 407 | 1% helix, 53% strand | Q9U3P2 |
Ligands and binding sites
- EMC · Ethyl mercury ion · ligand · 3 copies · chains D, E, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 28 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.56 | 0.84 | 26 | empty |
| 2 | 95 | 0.55 | 0.85 | 21 | empty |
| 3 | 106 | 0.54 | 0.84 | 25 | empty |
| 4 | 102 | 0.41 | 0.77 | 19 | empty |
| 5 | 62 | 0.38 | 0.79 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–D · 727 Ų buried · 11 hydrogen bonds · protein-protein
- C–F · 721 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 703 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 glycan, 18 disulfide (N-glycosylation, disulfide).
Compared structures
- 4OFY · Crystal Structure of the Complex of SYG-1 D1-D2 and SYG-2 D1-D4 · the same entry in another collection · chain C against C, TM-score 1.00
- B1Q236 · AlphaFold monomer V2.0 prediction for synaptogenesis protein syg-1 (B1Q236) · a predicted model of the same protein · chain B against A, TM-score 0.96
- Q9U3P2 · AlphaFold monomer V2.0 prediction for synaptogenesis protein syg-2 (Q9U3P2) · a predicted model of the same protein · chain D against A, TM-score 0.93
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 B1Q236
- Every structure of UniProt Q9U3P2
- Elsewhere: RCSB PDB 4OFY · PDBe 4OFY · UniProt B1Q236 · UniProt Q9U3P2
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