MolNFT v1 · #128299 · protein
Structure of pipy, the COG0325 family member of synechococcus elongatus PCC7942, with plp bound
5NM8: “Structure of pipy, the COG0325 family member of synechococcus elongatus PCC7942, with plp bound”. X-ray diffraction, 2 ligands (PLP, CA), 4 pockets (best druggability 0.52). MolNFT v1 #128299 on GenesisL1: 3D structure, binding…
- 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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