Research workbench
Pyrococcus furiosus mcm N-terminal domain F179A point mutant pentameric ring
Analyse Pyrococcus furiosus mcm N-terminal domain F179A point mutant pentameric ring in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YWL
- Type
- protein
- Length
- 2,540 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division control protein 21
- UniProt
- Q8U3I4
- Ligands
- ZN, SO4
- Pockets
- 20 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | Cell division control protein 21 | protein | 254 | 29% helix, 33% strand | Q8U3I4 |
Ligands and binding sites
- ZN · Zinc ion · metal · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, C, D, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 447 | 0.66 | 0.79 | 62 | empty |
| 2 | 244 | 0.66 | 0.84 | 24 | empty |
| 3 | 280 | 0.66 | 0.82 | 30 | empty |
| 4 | 302 | 0.66 | 0.82 | 31 | empty |
| 5 | 257 | 0.66 | 0.83 | 27 | empty |
Interfaces
15 interfaces between chains.
- C–D · 869 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 866 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 863 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 862 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 855 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4YWL · Pyrococcus furiosus MCM N-terminal domain F179A point mutant pentameric ring · the same entry in another collection · chain A against A, 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
- Every structure of UniProt Q8U3I4
- Elsewhere: RCSB PDB 4YWL · PDBe 4YWL · UniProt Q8U3I4
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