MolNFT v1 · #115929 · protein

Structure of XOO1075, a peptide deformylase from xanthomonas oryze pv oryze, in complex with fragment 275

5CY7: “Structure of XOO1075, a peptide deformylase from xanthomonas oryze pv oryze, in complex with fragment 275”. X-ray diffraction, 3 ligands (56U, CD, NA), 1 pocket (best druggability 0.58). MolNFT v1 #115929 on GenesisL1: 3D structure…

PDB: 5CY7
Type: protein
Length: 171 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: 56U, CD, NA
Pockets: 1 · best druggability 0.58

Structure

x-ray diffraction · 1 distinct chain · 26% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peptide deformylase (EC 3.5.1.88)	protein	171	26% helix, 30% strand	Q5H3Z2

Ligands and binding sites

56U · 2-(difluoromethyl)-1H-benzimidazole · 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

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	179	0.58	0.82	34	56U

Compared structures

5CY7 · Structure of Xoo1075, a peptide deformylase from Xanthomonas oryze pv oryze, in complex… · 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 5CY7 · PDBe 5CY7 · UniProt Q5H3Z2

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