Research workbench
Structure of pipy, the COG0325 family member of synechococcus elongatus PCC7942, with plp bound
Analyse Structure of pipy, the COG0325 family member of synechococcus elongatus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NM8
- Type
- protein
- Length
- 429 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pipy
- UniProt
- Q31LH9
- Ligands
- PLP, CA
- Pockets
- 4 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pipy | protein | 217 | 45% helix, 18% strand | Q31LH9 |
| B | Pipy | protein | 212 | 44% helix, 18% strand | Q31LH9 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.52 | 0.83 | 20 | empty |
| 2 | 192 | 0.52 | 0.78 | 38 | PLP |
| 3 | 114 | 0.42 | 0.76 | 29 | PLP |
| 4 | 61 | 0.37 | 0.78 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 555 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5NM8 · Structure of PipY, the COG0325 family member of Synechococcus elongatus PCC7942, with PLP… · 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 Q31LH9
- Elsewhere: RCSB PDB 5NM8 · PDBe 5NM8 · UniProt Q31LH9
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