3WFH | pdb_00003wfh

Crystal structure of anti-Prostaglandin E2 Fab fragment PGE2 complex

PDB DOI: https://doi.org/10.2210/pdb3WFH/pdb

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

Deposited: 2013-07-19 Released: 2014-07-23
Deposition Author(s): Sugahara, M., Ago, H., Saino, H., Miyano, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.200 (Depositor), 0.201 (DCC)
R-Value Work:
0.168 (Depositor), 0.169 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
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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: 47.53 kDa
Atom Count: 3,906
Modeled Residue Count: 427
Deposited Residue Count: 433
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mAb Fab H fragment	A	217	Mus musculus	Mutation(s): 0

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
mAb Fab L fragment	B	216	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P2E Query on P2E Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	(Z)-7-[(1R,2R,3R)-3-hydroxy-2-[(E,3S)-3-hydroxyoct-1-enyl]-5-oxo-cyclopentyl]hept-5-enoic acid C₂₀ H₃₂ O₅ XEYBRNLFEZDVAW-ARSRFYASSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.200 (Depositor), 0.201 (DCC)
R-Value Work: 0.168 (Depositor), 0.169 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.26	α = 90
b = 82.53	β = 90
c = 82.74	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-07-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-07-23
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary

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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.