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A new pii protein structure
Analyse A new pii protein structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MHY
- Type
- protein
- Length
- 327 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pii-like protein pz
- UniProt
- P70731
- Ligands
- ATP, AKG, MG
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pii-like protein pz | protein | 103 | 28% helix, 36% strand | P70731 |
| B, C | Pii-like protein pz | protein | 112 | 29% helix, 33% strand | P70731 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, C, B
- AKG · 2-oxoglutaric acid · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 4 copies · chains A, B, C
- PG6 · 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane · additive · 3 copies · chains A, C, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 210 | 0.78 | 0.93 | 35 | ATP, AKG, MG |
| 2 | 201 | 0.77 | 0.92 | 34 | ATP, AKG, MG |
| 3 | 193 | 0.76 | 0.91 | 36 | ATP, AKG, MG |
| 4 | 86 | 0.39 | 0.77 | 22 | PG6 |
| 5 | 52 | 0.34 | 0.78 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1238 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1215 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1196 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 3MHY · A New PII Protein Structure · 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 P70731
- Elsewhere: RCSB PDB 3MHY · PDBe 3MHY · UniProt P70731
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