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K2U complex structure of peptide deformylase from xanthomonas oryzae pv. oryzae

Analyse K2U complex structure of peptide deformylase from xanthomonas oryzae pv. oryzae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6IKY
Type: protein
Length: 160 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: K2U, NI
Pockets: 2 · best druggability 0.49

Structure

x-ray diffraction · 1 distinct chain · 28% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peptide deformylase (EC 3.5.1.88)	protein	160	28% helix, 33% strand	Q5H3Z2

Ligands and binding sites

K2U · (3~{R},4~{R})-4-oxidanyl-3-(phenylmethyl)-4-(phenylmethylsulfanyl)butanoic acid · ligand · chains A
NI · Nickel (II) ion · metal · 3 copies · 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	143	0.49	0.79	23	K2U
2	54	0.28	0.74	13	empty

Modifications

Observed in the structure: 1 modified (oxidation).

Compared structures

6IKY · K2U complex structure of peptide deformylase from Xanthomonas oryzae pv. oryzae · 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 6IKY · PDBe 6IKY · UniProt Q5H3Z2

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