Research workbench
Crystal structure of protein scalloped (222-440) bound to protein vestigial (298-337)
Analyse Crystal structure of protein scalloped (222-440) bound to protein vestigial… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y20
- Type
- protein
- Length
- 489 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein scalloped; Protein vestigial
- UniProt
- P30052, Q26366
- Ligands
- ACE, MYR, NH2
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein scalloped | protein | 213 | 16% helix, 51% strand | P30052 |
| B | Protein scalloped | protein | 208 | 17% helix, 52% strand | P30052 |
| C | Protein vestigial | protein | 33 | 58% helix, 0% strand | Q26366 |
| D | Protein vestigial | protein | 35 | 54% helix, 0% strand | Q26366 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, B, C, D
- MYR · Myristic acid · ligand · chains B
- NH2 · Amino group · ion · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.84 | 0.96 | 35 | MYR |
| 2 | 447 | 0.66 | 0.78 | 53 | ACE |
| 3 | 60 | 0.65 | 0.94 | 21 | empty |
| 4 | 59 | 0.43 | 0.83 | 15 | empty |
| 5 | 86 | 0.41 | 0.78 | 18 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1287 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1267 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 933 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 133 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 81 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
- 6Y20 · Crystal structure of Protein Scalloped (222-440) bound to Protein Vestigial (298-337) · the same entry in another collection · chain D against D, TM-score 1.00
- P30052 · AlphaFold monomer V2.0 prediction for protein scalloped (P30052) · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q26366 · AlphaFold monomer V2.0 prediction for protein vestigial (Q26366) · a predicted model of the same protein · chain C against A, TM-score 0.62
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 P30052
- Every structure of UniProt Q26366
- Elsewhere: RCSB PDB 6Y20 · PDBe 6Y20 · UniProt P30052 · UniProt Q26366
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