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Crystal structure of a soluble fragment of poliovirus 2C ATPase (2.55 ångström)
Analyse Crystal structure of a soluble fragment of poliovirus 2C ATPase (2.55 ångström) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Z3Q
- Type
- protein
- Length
- 1,086 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pv-2C
- EC
- 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48
- UniProt
- P03300
- Ligands
- ZN, PO4
- Pockets
- 12 · best druggability 0.71
Structure
x-ray diffraction · 6 distinct chains · 32% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Pv-2C (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 204 | 30% helix, 20% strand | P03300 |
| A | Pv-2C (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 202 | 30% helix, 19% strand | P03300 |
| D | Pv-2C (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 202 | 34% helix, 18% strand | P03300 |
| C | Pv-2C (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 188 | 30% helix, 20% strand | P03300 |
| E | Pv-2C (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 201 | 30% helix, 18% strand | P03300 |
| H | Pv-2C (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 89 | 44% helix, 7% strand | P03300 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains B, A, D, C, E, H
- PO4 · Phosphate ion · ion · 3 copies · chains B, A, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 804 | 0.71 | 0.77 | 65 | empty |
| 2 | 1193 | 0.69 | 0.74 | 75 | PO4 |
| 3 | 745 | 0.64 | 0.74 | 52 | PO4 |
| 4 | 234 | 0.47 | 0.74 | 22 | empty |
| 5 | 121 | 0.44 | 0.77 | 31 | empty |
Interfaces
7 interfaces between chains.
- D–E · 649 Ų buried · 1 hydrogen bond · protein-protein
- B–A · 636 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 560 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 481 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 469 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5Z3Q · Crystal Structure of a Soluble Fragment of Poliovirus 2C ATPase (2.55 Angstrom) · the same entry in another collection · chain B against B, 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 P03300
- Elsewhere: RCSB PDB 5Z3Q · PDBe 5Z3Q · UniProt P03300
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