MolNFT v1 · #128267 · protein

Structure of pipy, the COG0325 family member of synechococcus elongatus PCC7942,WITHOUT plp

5NLC: “Structure of pipy, the COG0325 family member of synechococcus elongatus PCC7942,WITHOUT plp”. X-ray diffraction, 1 ligand (PO4), 4 pockets (best druggability 0.51). MolNFT v1 #128267 on GenesisL1: 3D structure, binding sites and…

PDB: 5NLC
Type: protein
Length: 431 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pipy
UniProt: Q31LH9
Ligands: PO4
Pockets: 4 · best druggability 0.51

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pipy	protein	216	44% helix, 18% strand	Q31LH9
B	Pipy	protein	215	44% helix, 18% strand	Q31LH9

Ligands and binding sites

PO4 · Phosphate ion · ion · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	160	0.51	0.79	32	empty
2	188	0.49	0.76	32	empty
3	107	0.47	0.79	20	empty
4	59	0.29	0.75	13	empty

Interfaces

1 interface between chains.

A–B · 538 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

5NLC · Structure of PipY, the COG0325 family member of Synechococcus elongatus PCC7942,without… · 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 5NLC · PDBe 5NLC · UniProt Q31LH9

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