6GXB

Carbonic Anhydrase CAIX mimic in complex with inhibitor JS13

PDB DOI: https://doi.org/10.2210/pdb6GXB/pdb

Classification: LYASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-06-27 Released: 2019-05-08
Deposition Author(s): Brynda, J., Rezacova, P., Pospisilova, K.
Funding Organization(s): Czech Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free:
0.154 (Depositor), 0.160 (DCC)
R-Value Work:
0.113 (Depositor), 0.120 (DCC)
R-Value Observed:
0.114 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Inhibitor-Polymer Conjugates as a Versatile Tool for Detection and Visualization of Cancer-Associated Carbonic Anhydrase Isoforms

Pospisilova, K., Knedlik, T., Brynda, J., Rezacova, P., Sacha, P., Schimer, J., Kral, V., Cigler, P., Navratil, V., Subr, V., Konvalinka, J.

(2019) ACS Omega 4: 6746-6756

DOI: https://doi.org/10.1021/acsomega.9b00596

Macromolecule Content

Total Structure Weight: 29.33 kDa
Atom Count: 2,429
Modelled Residue Count: 257
Deposited Residue Count: 257
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	257	Homo sapiens	Mutation(s): 0 Gene Names: CA2 EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens) Explore P00918 Go to UniProtKB: P00918
PHAROS: P00918 GTEx: ENSG00000104267
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00918
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FF5 Query on FF5 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]	~{N}-[4-[4-[(4-sulfamoylphenyl)carbamoylamino]phenoxy]butyl]ethanamide C₁₉ H₂₄ N₄ O₅ S CDBPPECJGAINPA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.154 (Depositor), 0.160 (DCC)
R-Value Work: 0.113 (Depositor), 0.120 (DCC)
R-Value Observed: 0.114 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.82	α = 90
b = 41.15	β = 103.81
c = 72.01	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-05-08

Deposition Author(s):

Pospisilova, K.

Funding Organization	Location	Grant Number
Czech Science Foundation	Czech Republic	GA15-05677S

Revision History (Full details and data files)

Version 1.0: 2019-05-08
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Refinement description

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.