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Structure of XOO1075, a peptide deformyase from xanthomonas oryzae pv. oryze, in complex with fragment 493

Analyse Structure of XOO1075, a peptide deformyase from xanthomonas oryzae pv. oryze… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5CVK
Type: protein
Length: 169 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: 56E, CD, NA
Pockets: 1 · best druggability 0.55

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	169	26% helix, 34% strand	Q5H3Z2

Ligands and binding sites

56E · ethyl N-[(5-methylthiophen-3-yl)carbonyl]glycinate · ligand · chains A
CD · Cadmium ion · metal · 5 copies · chains A
NA · Sodium ion · metal · chains A
ACT · Acetate ion · 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	217	0.55	0.78	41	56E, CD

Compared structures

5CVK · Structure of Xoo1075, a peptide deformyase from Xanthomonas oryzae pv. oryze, in complex… · the same entry in another collection · chain A against A, TM-score 1.00

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Every structure of UniProt Q5H3Z2
Elsewhere: RCSB PDB 5CVK · PDBe 5CVK · UniProt Q5H3Z2

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