MolNFT v1 · #119238 · protein

The structure of kdgf from yersinia enterocolitica with malonate bound in the active site.

5FPZ · Pectin degradation protein: “The structure of kdgf from yersinia enterocolitica with malonate bound in the active site.”. X-ray diffraction, 1 ligand (NI), 1 pocket (best druggability 0.58). MolNFT v1 #119238 on GenesisL1: 3D…

PDB: 5FPZ
Type: protein
Length: 110 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pectin degradation protein
UniProt: A1JMF7
Ligands: NI
Pockets: 1 · best druggability 0.58

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 57% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pectin degradation protein	protein	110	5% helix, 57% strand	A1JMF7

Ligands and binding sites

NI · Nickel (II) ion · metal · chains A
MLA · Malonic acid · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	158	0.58	0.82	23	MLA

Compared structures

5FPZ · The structure of KdgF from Yersinia enterocolitica with malonate bound in the active site. · 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 A1JMF7
Elsewhere: RCSB PDB 5FPZ · PDBe 5FPZ · UniProt A1JMF7

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