wwPDB validation report of PDB entry 2XAD

N-ACYL GLM PEUDO-TEICOPLANIN DEACETYLASE

CRYSTAL STRUCTURE OF DEACETYLASE-BOG COMPLEX IN BIOSYNTHESIS PATHWAY OF TEICOPLANIN.

THE COMPLEXED CRYSTAL STRUCTURE OF THE PRIMARY HEXOSE OXIDASE (DBV29) IN ANTIBIOTIC A40926 BIOSYNTHESIS

ENGINEERED RESIDUE IN CHAIN A, HIS 164 TO ASN
ENGINEERED RESIDUE IN CHAIN B, HIS 164 TO ASN
ENGINEERED RESIDUE IN CHAIN C, HIS 164 TO ASN
ENGINEERED RESIDUE IN CHAIN D, HIS 164 TO ASN

TEICPLANIN IS A FAMILY OF TETRACYCLIC GLYCOPEPTIDE ANTIBIOTICS.
THE SCAFFOLD IS A HEPTAPEPTIDE FURTHER GLYCOSYLATED BY THREE
MONO SACCHARIDES: MANNOSE, N-ACETYLGLUCOSAMINE AND
BETA-D-GLUCOSAMINE AND ONLY DIFFER BY THE SIDE CHAIN ATTACHED
TO THE LATTER.
HERE, TEICPLANIN IS REPRESENTED BY GROUPING TOGETHER THE SEQUENCE
(SEQRES) AND 4 LIGANDS (HET).

GROUP: 1
NAME: TEICPLANIN
CHAIN: E, F, G, H
COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 701 TO 707
COMPONENT_2: SUGAR RESIDUES 708, 709 AND 710
COMPONENT_3: FATTY ACID RESIDUE 711

DESCRIPTION: TEICPLANIN IS A TETRACYCLIC HEPTAPEPTIDE
GLYCOSYLATED BY THREE MONOSCCARIDES, RESIDUES 708, 709
AND 710, ON RESIDUES 707, 706 AND 704, RESPECTIVELY. THE FATTY
ACID IS LINKED TO THE BETA-D-GLUCOSAMINE (RESIDUE 710)

HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY

Crystal structure of deacetylase-teicoplanin complex in biosynthesis pathway of teicoplanin

The analyses of the Patterson function reveals a significant off-origin peak that is 59.45 % of the origin peak, indicating pseudo-translational symmetry. The chance of finding a peak of this or larger height by random in a structure without pseudo-translational symmetry is equal to 1.7616e-05. The detected translational NCS is most likely also responsible for the elevated intensity ratio. See the relevant section of the logfile for more details.

20191225.v01 (using entries in the PDB archive December 25th 2019)
structure factor analysis and validation
geometric validation package for ligand chemistry in protein x-ray structures