Research workbench
Structure of PNOB8 para
Analyse Structure of PNOB8 para in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K5Z
- Type
- protein
- Length
- 1,217 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Para
- UniProt
- O93708
- Ligands
- ANP, MG
- Pockets
- 17 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Para | protein | 310 | 44% helix, 16% strand | O93708 |
| B | Para | protein | 302 | 42% helix, 17% strand | O93708 |
| C | Para | protein | 291 | 37% helix, 17% strand | O93708 |
| D | Para | protein | 314 | 45% helix, 16% strand | O93708 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, D
- MG · Magnesium ion · metal · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 232 | 0.82 | 0.95 | 39 | ANP, MG |
| 2 | 231 | 0.82 | 0.95 | 38 | ANP, MG |
| 3 | 1099 | 0.76 | 0.78 | 91 | empty |
| 4 | 267 | 0.60 | 0.79 | 38 | empty |
| 5 | 143 | 0.53 | 0.81 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2028 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1646 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 675 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 635 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 598 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5K5Z · Structure of pnob8 ParA · 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 O93708
- Elsewhere: RCSB PDB 5K5Z · PDBe 5K5Z · UniProt O93708
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