Research workbench
Crystal structure of the SYCP1 C-terminal back-to-back assembly
Analyse Crystal structure of the SYCP1 C-terminal back-to-back assembly in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F63
- Type
- protein
- Length
- 383 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Synaptonemal complex protein 1
- UniProt
- Q15431
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 98% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Synaptonemal complex protein 1 | protein | 96 | 98% helix, 0% strand | Q15431 |
| C | Synaptonemal complex protein 1 | protein | 96 | 97% helix, 0% strand | Q15431 |
| D | Synaptonemal complex protein 1 | protein | 95 | 98% helix, 0% strand | Q15431 |
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 | 90 | 0.73 | 0.95 | 20 | empty |
| 2 | 115 | 0.65 | 0.89 | 29 | empty |
| 3 | 60 | 0.53 | 0.87 | 12 | empty |
| 4 | 101 | 0.49 | 0.81 | 16 | empty |
| 5 | 51 | 0.48 | 0.86 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2256 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 2232 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 2026 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1874 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 807 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6F63 · Crystal structure of the SYCP1 C-terminal back-to-back assembly · the same entry in another collection · chain A against A, TM-score 1.00
- Q15431 · AlphaFold monomer V2.0 prediction for synaptonemal complex protein 1 (Q15431) · a predicted model of the same protein · chain C against A, TM-score 0.84
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 Q15431
- Elsewhere: RCSB PDB 6F63 · PDBe 6F63 · UniProt Q15431
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