MolNFT v1 · #146292 · protein
Structure of mouse SYCP3, P21 form
6DD8 · Synaptonemal complex protein 3: “Structure of mouse SYCP3, P21 form”. X-ray diffraction, 4 pockets (best druggability 0.77). MolNFT v1 #146292 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6DD8
- Type
- protein
- Length
- 494 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Synaptonemal complex protein 3
- UniProt
- A2RSE7
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 94% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Synaptonemal complex protein 3 | protein | 131 | 92% helix, 0% strand | A2RSE7 |
| B | Synaptonemal complex protein 3 | protein | 123 | 92% helix, 0% strand | A2RSE7 |
| C | Synaptonemal complex protein 3 | protein | 123 | 97% helix, 0% strand | A2RSE7 |
| D | Synaptonemal complex protein 3 | protein | 117 | 97% helix, 0% strand | A2RSE7 |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 99 | 0.77 | 0.97 | 18 | empty |
| 2 | 269 | 0.65 | 0.82 | 35 | empty |
| 3 | 120 | 0.49 | 0.80 | 19 | empty |
| 4 | 62 | 0.30 | 0.75 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2824 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 2653 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 2541 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 2427 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 1202 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 modified (engineered).
Compared structures
- 6DD8 · Structure of mouse SYCP3, P21 form · the same entry in another collection · chain A against A, TM-score 1.00
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 A2RSE7
- Elsewhere: RCSB PDB 6DD8 · PDBe 6DD8 · UniProt A2RSE7
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