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Structure of the archaeal beta-casp protein with N-terminal kh domains from methanothermobacter thermautotrophicus
Analyse Structure of the archaeal beta-casp protein with N-terminal kh domains from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YCB
- Type
- protein
- Length
- 1,269 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cleavage and polyadenylation specificity factor
- UniProt
- O27271
- Ligands
- ZN, K, PO4
- Pockets
- 18 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cleavage and polyadenylation specificity factor | protein | 634 | 37% helix, 21% strand | O27271 |
| B | Cleavage and polyadenylation specificity factor | protein | 635 | 37% helix, 21% strand | O27271 |
Ligands and binding sites
- ZN · Zinc ion · metal · 5 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 407 | 0.77 | 0.86 | 58 | PO4 |
| 2 | 562 | 0.77 | 0.84 | 74 | PO4 |
| 3 | 869 | 0.76 | 0.80 | 86 | PO4 |
| 4 | 645 | 0.74 | 0.80 | 64 | empty |
| 5 | 338 | 0.62 | 0.78 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 1016 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 2YCB · Structure of the archaeal beta-CASP protein with N-terminal KH domains from… · 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 O27271
- Elsewhere: RCSB PDB 2YCB · PDBe 2YCB · UniProt O27271
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