4YVY | pdb_00004yvy

Crystal structure of human carbonic anhydrase II in complex with hydroxylamine-O-sulfonamide, a molecule incorporating two zinc-binding groups.

PDB DOI: https://doi.org/10.2210/pdb4YVY/pdb

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

Deposited: 2015-03-20 Released: 2016-03-30
Deposition Author(s): Di Fiore, A., De Simone, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.192 (Depositor), 0.200 (DCC)
R-Value Work:
0.162 (Depositor), 0.170 (DCC)

wwPDB Validation 3D Report Full Report

Validation slider image for 4YVY

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

Literature

A VERSATILE ZINC-BINDING GROUP FOR CARBONIC ANHYDRASE INHIBITORS

Di Fiore, A., Vergara, A., Caterino, M., Alterio, V., Monti, S.M., Ombouma, J., Dumy, P., Vullo, D., Supurand, C.T., Winum, J.-Y., De Simone, G.

To be published.

Macromolecule Content

Total Structure Weight: 29.34 kDa
Atom Count: 2,436
Modeled Residue Count: 256
Deposited Residue Count: 259
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	259	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4J3 Query on 4J3 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]	amino(aminooxy)sulfane dioxide H₄ N₂ O₃ S BTXCHYCUHBGRMK-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: 1.45 Å
R-Value Free: 0.192 (Depositor), 0.200 (DCC)
R-Value Work: 0.162 (Depositor), 0.170 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.236	α = 90
b = 41.319	β = 104.39
c = 72.153	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	refinement

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-03-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-03-30
Type: Initial release
Version 1.1: 2024-05-08
Changes: Data collection, Database references, Derived calculations

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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.