Research workbench
Ski-like protein
Analyse Ski-like protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C4V
- Type
- protein
- Length
- 856 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mothers against decapentaplegic homolog 4; Ski-like protein
- UniProt
- Q13485, P12757
- Ligands
- ZN, NI
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 27% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mothers against decapentaplegic homolog 4 | protein | 192 | 28% helix, 31% strand | Q13485 |
| C | Mothers against decapentaplegic homolog 4 | protein | 188 | 26% helix, 32% strand | Q13485 |
| E | Mothers against decapentaplegic homolog 4 | protein | 196 | 27% helix, 31% strand | Q13485 |
| B | Ski-like protein | protein | 96 | 27% helix, 22% strand | P12757 |
| D | Ski-like protein | protein | 91 | 27% helix, 22% strand | P12757 |
| F | Ski-like protein | protein | 93 | 28% helix, 22% strand | P12757 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains B, D, F
- NI · Nickel (II) ion · metal · 2 copies · chains B
- GOL · Glycerol · additive · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1106 | 0.86 | 0.87 | 116 | GOL |
| 2 | 705 | 0.72 | 0.79 | 92 | empty |
| 3 | 718 | 0.71 | 0.78 | 73 | empty |
| 4 | 77 | 0.51 | 0.84 | 21 | empty |
| 5 | 80 | 0.47 | 0.82 | 31 | empty |
Interfaces
8 interfaces between chains.
- A–B · 963 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 946 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 799 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 798 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 752 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5C4V · Ski-like protein · the same entry in another collection · chain F against F, TM-score 1.00
- Q13485 · AlphaFold monomer V2.0 prediction for mothers against decapentaplegic homolog 4 (Q13485) · a predicted model of the same protein · chain C against A, TM-score 0.99
- P12757 · AlphaFold monomer V2.0 prediction for ski-like protein (P12757) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q13485
- Every structure of UniProt P12757
- Elsewhere: RCSB PDB 5C4V · PDBe 5C4V · UniProt Q13485 · UniProt P12757
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