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Structure of XOO1075, a peptide deformylase from xanthomonas oryze pv oryzae, in complex with fragment 83

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

PDB: 5CWY
Type: protein
Length: 168 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: 4WL, CD, NA
Pockets: 2 · best druggability 0.58

Structure

x-ray diffraction · 1 distinct chain · 26% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peptide deformylase (EC 3.5.1.88)	protein	168	26% helix, 31% strand	Q5H3Z2

Ligands and binding sites

4WL · 4H-thieno[3,2-b]pyrole-5-carboxylic acid · ligand · chains A
CD · Cadmium ion · metal · 3 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

2 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	107	0.58	0.85	23	4WL
2	54	0.26	0.73	14	empty

Compared structures

5CWY · Structure of Xoo1075, a peptide deformylase from Xanthomonas oryze pv oryzae, 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 5CWY · PDBe 5CWY · UniProt Q5H3Z2

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