3WIF | pdb_00003wif

Crystal structure of anti-prostaglandin E2 Fab fragment 9Cl-PGF2beta complex

PDB DOI: https://doi.org/10.2210/pdb3WIF/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus
Mutation(s): No

Deposited: 2013-09-12 Released: 2014-09-17
Deposition Author(s): Sugahara, M., Ago, H., Saino, H., Miyano, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.190 (Depositor), 0.193 (DCC)
R-Value Work:
0.172 (Depositor), 0.174 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3WIF

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of anti-Prostaglandin E2 Fab fragment with Prostaglandin E2

Sugahara, M., Ago, H., Saino, H., Miyano, M., Kurahashi, Y., Aoyama, S., Takehira, M., Yutani, K., Yamamoto, S.

To be published.

Macromolecule Content

Total Structure Weight: 47.78 kDa
Atom Count: 4,079
Modeled Residue Count: 427
Deposited Residue Count: 435
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mAb Fab H fragment	A	218	Mus musculus	Mutation(s): 0

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
mAb Fab L fragment	B	217	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ON5 Query on ON5 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(Z)-7-[(1R,2R,3R,5R)-5-chloranyl-3-oxidanyl-2-[(E,3S)-3-oxidanyloct-1-enyl]cyclopentyl]hept-5-enoic acid C₂₀ H₃₃ Cl O₄ RDZUDQFNGNUIKH-JZFBHDEDSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.190 (Depositor), 0.193 (DCC)
R-Value Work: 0.172 (Depositor), 0.174 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.66	α = 90
b = 82.31	β = 90
c = 82.56	γ = 90

Software Package:

Software Name	Purpose
BSS	data collection
MOLREP	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-09-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-09-17
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-10-30
Changes: Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.