6BL4
Crystal Complex of Cyclooxygenase-2 with indomethacin-ethylenediamine-dansyl conjugate
- PDB DOI: https://doi.org/10.2210/pdb6BL4/pdb
- Classification: OXIDOREDUCTASE/INHIBITOR
- Organism(s): Mus musculus
- Expression System: Spodoptera frugiperda
- Mutation(s): No 
- Membrane Protein: Yes  mpstruc
- Deposited: 2017-11-09 Released: 2018-11-14 
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.22 Å
- R-Value Free: 0.220 
- R-Value Work: 0.189 
- R-Value Observed: 0.190 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Prostaglandin G/H synthase 2 | 587 | Mus musculus | Mutation(s): 0  Gene Names: Ptgs2, Cox-2, Cox2, Pghs-b, Tis10 EC: 1.14.99.1 Membrane Entity: Yes  | ||
UniProt | |||||
Find proteins for Q05769 (Mus musculus) Explore Q05769  Go to UniProtKB:  Q05769 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q05769 | ||||
Sequence AnnotationsExpand | |||||
|
Oligosaccharides
Small Molecules
Ligands 4 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
DXS Query on DXS | AA [auth D], L [auth A], R [auth B], V [auth C] | 2-[1-(4-chlorobenzene-1-carbonyl)-5-methoxy-2-methyl-1H-indol-3-yl]-N-[2-({[5-(dimethylamino)naphthalen-1-yl]sulfonyl}amino)ethyl]acetamide C33 H33 Cl N4 O5 S GWNNEESLGDFXNP-UHFFFAOYSA-N | |||
HEM Query on HEM | I [auth A], O [auth B], S [auth C], X [auth D] | PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L | |||
BOG Query on BOG | BA [auth D], CA [auth D], M [auth A], N [auth A], W [auth C] | octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N | |||
NAG Query on NAG | J [auth A] K [auth A] P [auth B] Q [auth B] T [auth C] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.22 Å
- R-Value Free: 0.220 
- R-Value Work: 0.189 
- R-Value Observed: 0.190 
- Space Group: C 1 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 214.795 | α = 90 |
b = 120.414 | β = 123.6 |
c = 134.417 | γ = 90 |
Software Name | Purpose |
---|---|
Aimless | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2018-11-14  Deposition Author(s): Xu, S., Uddin, M.J., Banerjee, S., Marnett, L.J.
Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | -- |
National Institutes of Health/National Cancer Institute (NIH/NCI) | United States | -- |
Revision History (Full details and data files)
- Version 1.0: 2018-11-14
Type: Initial release - Version 1.1: 2019-02-20
Changes: Author supporting evidence, Data collection - Version 1.2: 2019-03-13
Changes: Data collection - Version 1.3: 2019-05-15
Changes: Data collection, Database references - Version 1.4: 2019-06-12
Changes: Data collection, Database references - Version 1.5: 2019-12-04
Changes: Author supporting evidence - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-10-04
Changes: Data collection, Database references, Refinement description, Structure summary