6GXE | pdb_00006gxe

Carbonic Anhydrase CAIX mimic in complex with inhibitor JS14

PDB DOI: https://doi.org/10.2210/pdb6GXE/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: 1.30 Å
R-Value Free:
0.154 (Depositor), 0.159 (DCC)
R-Value Work:
0.125 (Depositor), 0.126 (DCC)
R-Value Observed:
0.125 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6GXE

Ligand Structure Quality Assessment

This is version 1.2 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., Sacha, P., Kostka, L., Schimer, J., Brynda, J., Kral, V., Cigler, P., Navratil, V., Etrych, T., Subr, V., Kugler, M., Fabry, M., Rezacova, P., Konvalinka, J.

(2019) ACS Omega

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

Macromolecule Content

Total Structure Weight: 30.3 kDa
Atom Count: 2,363
Modeled Residue Count: 257
Deposited Residue Count: 257
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00918
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FFH Query on FFH Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	3-[2-[2-[2-[2-(aminomethyloxy)ethoxy]ethoxy]ethoxy]ethoxy]-~{N}-[4-[4-[(4-sulfamoylphenyl)carbamoylamino]phenoxy]butyl]propanamide C₂₉ H₄₅ N₅ O₁₀ S UDWQBPJNUHSQMR-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [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: 1.30 Å
R-Value Free: 0.154 (Depositor), 0.159 (DCC)
R-Value Work: 0.125 (Depositor), 0.126 (DCC)
R-Value Observed: 0.125 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.92	α = 90
b = 41.22	β = 103.89
c = 72.11	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

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: 2019-12-25
Changes: Data collection
Version 1.2: 2024-05-15
Changes: Data collection, Database references

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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.