Research workbench
Crystal structure of the chromoprotein spispink
Analyse Crystal structure of the chromoprotein spispink in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SWU
- Type
- protein
- Length
- 862 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chromoprotein spispink
- Ligands
- CIV
- Pockets
- 15 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Chromoprotein spispink | protein | 216 | 6% helix, 57% strand | — |
| D | Chromoprotein spispink | protein | 214 | 5% helix, 58% strand | — |
Ligands and binding sites
- CIV · 2-[2-[(1~{S})-1,5-bis(azanyl)pentyl]-4-[(4-hydroxyphenyl)methyl]-5-oxidanylidene-imidazol-1-yl]ethanamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 612 | 0.86 | 0.92 | 57 | empty |
| 2 | 65 | 0.73 | 0.98 | 22 | CIV |
| 3 | 59 | 0.73 | 0.99 | 22 | CIV |
| 4 | 64 | 0.73 | 0.98 | 24 | CIV |
| 5 | 676 | 0.72 | 0.79 | 51 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1213 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1211 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 930 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 918 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 146 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 7SWU · Crystal structure of the chromoprotein spisPINK · the same entry in another collection · chain C against C, 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
- Elsewhere: RCSB PDB 7SWU · PDBe 7SWU
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