Research workbench
Structure of CDC14 bound to SIC1 pxl motif
Analyse Structure of CDC14 bound to SIC1 pxl motif in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6G86
- Type
- protein
- Length
- 745 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein phosphatase CDC14; Protein SIC1
- EC
- 3.1.3.48
- UniProt
- Q00684, P38634
- Ligands
- ZN
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein phosphatase CDC14 (EC 3.1.3.48) | protein | 357 | 44% helix, 15% strand | Q00684 |
| B | Tyrosine-protein phosphatase CDC14 (EC 3.1.3.48) | protein | 367 | 43% helix, 14% strand | Q00684 |
| D | Protein SIC1 | protein | 10 | 0% helix, 0% strand | P38634 |
| C | Protein SIC1 | protein | 11 | 0% helix, 0% strand | P38634 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B
- P6G · Hexaethylene glycol · additive · 3 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 164 | 0.82 | 0.97 | 38 | empty |
| 2 | 202 | 0.57 | 0.79 | 24 | PEG |
| 3 | 189 | 0.56 | 0.79 | 23 | PEG |
| 4 | 142 | 0.48 | 0.78 | 21 | PEG |
| 5 | 136 | 0.47 | 0.78 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1763 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 636 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 532 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 6G86 · Structure of Cdc14 bound to SIC1 PxL motif · the same entry in another collection · chain C against C, TM-score 1.00
- Q00684 · AlphaFold monomer V2.0 prediction for tyrosine-protein phosphatase CDC14 (Q00684) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P38634 · AlphaFold monomer V2.0 prediction for protein SIC1 (P38634) · a predicted model of the same protein · chain D against A, TM-score 0.37
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 Q00684
- Every structure of UniProt P38634
- Elsewhere: RCSB PDB 6G86 · PDBe 6G86 · UniProt Q00684 · UniProt P38634
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