Research workbench
Crystal structure of spop bound with a peptide
Analyse Crystal structure of spop bound with a peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D3D
- Type
- protein
- Length
- 301 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Speckle-type poz protein; Glu-val-ser-ile-ile-gln-gly-ala-asp-ser-thr-thr
- UniProt
- O43791
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Speckle-type poz protein | protein | 139 | 12% helix, 50% strand | O43791 |
| a, b | Glu-val-ser-ile-ile-gln-gly-ala-asp-ser-thr-thr | protein | 12 | 0% helix, 42% strand | — |
| B | Speckle-type poz protein | protein | 138 | 14% helix, 52% strand | O43791 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 527 | 0.73 | 0.81 | 56 | empty |
| 2 | 140 | 0.42 | 0.75 | 25 | empty |
| 3 | 63 | 0.35 | 0.77 | 14 | empty |
Interfaces
4 interfaces between chains.
- A–a · 688 Ų buried · 22 hydrogen bonds · protein-protein
- B–b · 677 Ų buried · 24 hydrogen bonds · protein-protein
- A–b · 454 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 176 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
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 O43791
- Elsewhere: RCSB PDB 7D3D · PDBe 7D3D · UniProt O43791
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