wwPDB validation report of PDB entry 1PGG

1-(4-IODOBENZOYL)-5-METHOXY-2-METHYL INDOLE-3-ACETIC ACID

THIS SEQUENCE IS FOUND IN ENTRY 1PRH. THE NUMBERING IS DERIVED FROM THE PRE-PROTEIN, WHICH CONTAINS A 24-RESIDUE SIGNAL SEQUENCE WHICH IS CLEAVED DURING MATURATION. NOTE THAT THE FOLLOWING SEQUENCE CORRESPONDS ONLY TO THE RESIDUES SEEN IN THE EXPERIMENTAL ELECTRON DENSITY MAP, AND COMMENCES AT RESIDUE 33

THE STARTING MODEL FOR THIS REFINEMENT WAS THE 3.1 ANGSTROM REFINED CRYSTAL STRUCTURE OF THE PROSTAGLANDIN SYNTHASE-FLURBIPROFEN COMPLEX, FOR WHICH INDIVIDUAL ISOTROPIC ATOMIC TEMPERATURE FACTORS WERE REFINED. THESE B-VALUES WERE USED FOR THIS STRUCTURE WITHOUT FURTHER REFINEMENT.

THE LOW RESOLUTION OF THE IODOINDOMETHACIN COMPLEX STRUCTURE PRECLUDED REFINEMENT OF ALL ATOMIC POSITIONS. RATHER, THE TWO HALVES OF THE DIMER WERE SUBJECTED TO RIGID BODY REFINEMENT, SUBJECT TO NON-CRYSTALLOGRAPHIC SYMMETRY CONSTRAINTS. THE DRUG WAS THEN PLACED IN THE ACTIVE SITE, WHERE CLEAR ELECTRON DENSITY WAS SEEN FOR FOR THE IODINE ATOM ONLY. THE REMAINDER OF THE DRUG WAS CONSTRUCTED BY MODEL-BUILDING AND ITS POSITION REFINED BY RIGID BODY METHODS. THE EXPERIMENTAL ELECTRON DENSITY DOES NOT ALLOW FOR UNAMBIGUOUS POSITIONING OF THE LIGHT ATOMS OF THE INHIBITOR. AFTER RIGID BODY MINIMIZATION, THE STRUCTURE WAS FURTHER REFINED BY ALLOWING ONLY THOSE ATOMS WITHIN AN 8 ANGSTROM SPHERE CENTERED ON ON THE INHIBITOR TO MOVE. TWO POSSIBLE CONFORMATIONS OF THE DRUG WERE FOUND, BOTH OF WHICH WERE CONSISTENT WITH THE OBSERVED HEAVY ATOM DENSITY; THESE CORRESPOND TO THE CIS AND TRANS ROTATIONAL CONFORMERS OF THE DRUG. THIS FILE SHOWS THE RESULTS OF THE REFINEMENT OF THE TRANS MODEL.

PROSTAGLANDIN H2 SYNTHASE-1, PROTOPORPHYRIN IX CONTAINING FE, 1-(4-IODOBENZOYL)-5-METHOXY-2-METHYL INDOLE-3-ACETIC ACID
PROSTAGLANDIN H2 SYNTHASE-1 COMPLEXED WITH 1-(4-IODOBENZOYL)-5-METHOXY-2-METHYLINDOLE-3-ACETIC ACID (IODOINDOMETHACIN), TRANS MODEL

THE CYCLOOXYGENASE ACTIVE SITE IS LOCATED WITHIN A LONG HYDROPHOBIC CHANNEL AT A REGION DEFINED BY RESIDUES ARG 120, SER 530 (SITE OF ASPIRIN ACETYLATION), TYR 385, AND GLU 524. (A CHAIN)

THE PEROXIDASE ACTIVE SITE IS AT THE HEME (HEM 601) SITE. HIS 388 IS THE PROXIMAL HEME LIGAND. (A CHAIN)

THE CYCLOOXYGENASE ACTIVE SITE IS LOCATED WITHIN A LONG HYDROPHOBIC CHANNEL AT A REGION DEFINED BY RESIDUES ARG 120, SER 530 (SITE OF ASPIRIN ACETYLATION), TYR 385, AND GLU 524. (B CHAIN)

THE PEROXIDASE ACTIVE SITE IS AT THE HEME (HEM 601) SITE. HIS 388 IS THE PROXIMAL HEME LIGAND. (B CHAIN)

20191225.v01 (using entries in the PDB archive December 25th 2019)

geometric validation package for ligand chemistry in protein x-ray structures