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- PDB-1pgf: PROSTAGLANDIN H2 SYNTHASE-1 COMPLEXED WITH 1-(4-IODOBENZOYL)-5-ME... -

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Basic information

Entry
Database: PDB / ID: 1pgf
TitlePROSTAGLANDIN H2 SYNTHASE-1 COMPLEXED WITH 1-(4-IODOBENZOYL)-5-METHOXY-2-METHYLINDOLE-3-ACETIC ACID (IODOINDOMETHACIN), CIS MODEL
ComponentsPROSTAGLANDIN H2 SYNTHASE-1Cyclooxygenase
KeywordsOXIDOREDUCTASE / DIOXYGENASE / PEROXIDASE
Function / homology
Function and homology information


prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / cyclooxygenase pathway / prostaglandin biosynthetic process / dioxygenase activity / peroxidase activity / regulation of blood pressure / response to oxidative stress / intracellular membrane-bounded organelle / heme binding ...prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / cyclooxygenase pathway / prostaglandin biosynthetic process / dioxygenase activity / peroxidase activity / regulation of blood pressure / response to oxidative stress / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / protein homodimerization activity / metal ion binding / cytoplasm
Similarity search - Function
Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / EGF-like domain / Haem peroxidase superfamily / EGF-like domain profile. / EGF-like domain
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Chem-IMM / : / Prostaglandin G/H synthase 1
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodX-RAY DIFFRACTION / Resolution: 4.5 Å
AuthorsLoll, P.J. / Picot, D. / Garavito, R.M.
Citation
Journal: Biochemistry / Year: 1996
Title: Synthesis and use of iodinated nonsteroidal antiinflammatory drug analogs as crystallographic probes of the prostaglandin H2 synthase cyclooxygenase active site.
Authors: Loll, P.J. / Picot, D. / Ekabo, O. / Garavito, R.M.
#1: Journal: Nat.Struct.Biol. / Year: 1995
Title: The Structural Basis of Aspirin Activity Inferred from the Crystal Structure of Inactivated Prostaglandin H2 Synthase
Authors: Loll, P.J. / Picot, D. / Garavito, R.M.
#2: Journal: Nature / Year: 1994
Title: The X-Ray Crystal Structure of the Membrane Protein Prostaglandin H2 Synthase-1
Authors: Picot, D. / Loll, P.J. / Garavito, R.M.
History
DepositionDec 2, 1995Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROSTAGLANDIN H2 SYNTHASE-1
B: PROSTAGLANDIN H2 SYNTHASE-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,19512
Polymers132,3302
Non-polymers3,86510
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11240 Å2
ΔGint-39 kcal/mol
Surface area40980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.220, 208.990, 232.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.995539, -0.058457, 0.074057), (-0.058971, -0.227185, -0.972064), (0.073648, -0.972095, 0.222725)
Vector: 82.149, 233.85699, 180.989)

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Components

#1: Protein PROSTAGLANDIN H2 SYNTHASE-1 / Cyclooxygenase / CYCLOOXYGENASE I


Mass: 66164.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organelle: SEMINAL VESICLESeminal vesicles
References: PIR: A29947, UniProt: P05979*PLUS, prostaglandin-endoperoxide synthase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical ChemComp-IMM / 1-(4-IODOBENZOYL)-5-METHOXY-2-METHYL INDOLE-3-ACETIC ACID


Mass: 449.239 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H16INO4
Sequence detailsTHIS SEQUENCE IS FOUND IN ENTRY 1PRH. THE NUMBERING IS DERIVED FROM THE PRE-PROTEIN, WHICH CONTAINS ...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.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.55 Å3/Da / Density % sol: 72 %
Crystal grow
*PLUS
Method: other
Details: Garavito, R.M., (1995) J. Biomembr. Bioenerg., 28, 13.

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Dec 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 4.5→50 Å / Num. obs: 11169 / % possible obs: 79.7 % / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Rmerge(I) obs: 0.102
Reflection
*PLUS
Lowest resolution: 15 Å / Num. measured all: 15439

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Processing

Software
NameVersionClassification
MADNESdata collection
X-PLOR3.1model building
X-PLOR3.1refinement
MADNESdata reduction
X-PLOR3.1phasing
RefinementResolution: 4.5→8 Å / σ(F): 1
Details: 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 ...Details: 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 ENTRY SHOWS THE RESULTS OF THE REFINEMENT OF THE CIS MODEL.
RfactorNum. reflection% reflection
Rfree0.267 945 10 %
Rwork0.254 --
obs0.254 8235 79.2 %
Displacement parametersBiso mean: 22.2 Å2
Refinement stepCycle: LAST / Resolution: 4.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8954 0 248 0 9202
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.99
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.73
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.73

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