MolNFT v1 · #115628 · protein

Methionine-alanine complex structure of peptide deformylase from xanthomonas oryzae pv. oryzae

5CPD: “Methionine-alanine complex structure of peptide deformylase from xanthomonas oryzae pv. oryzae”. X-ray diffraction, 2 ligands (CD, NA), 1 pocket (best druggability 0.27). MolNFT v1 #115628 on GenesisL1: 3D structure, binding sites…

PDB: 5CPD
Type: protein
Length: 170 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptide deformylase
EC: 3.5.1.88
UniProt: Q5H3Z2
Ligands: CD, NA
Pockets: 1 · best druggability 0.27

Structure

x-ray diffraction · 1 distinct chain · 26% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peptide deformylase (EC 3.5.1.88)	protein	170	26% helix, 34% strand	Q5H3Z2

Ligands and binding sites

CD · Cadmium ion · metal · 3 copies · chains A
NA · Sodium ion · metal · 2 copies · chains A
ACT · Acetate ion · additive · chains A
GOL · Glycerol · 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	50	0.27	0.74	13	empty

Modifications

Observed in the structure: 1 modified (oxidation).

Compared structures

5CPD · Methionine-alanine complex structure of peptide deformylase from Xanthomonas oryzae pv.… · 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 Q5H3Z2
Elsewhere: RCSB PDB 5CPD · PDBe 5CPD · UniProt Q5H3Z2

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