5OHH

Crystal structure of human carbonic anhydrase isozyme XIII with 2-[(1S)-2,3-Dihydro-1H-inden-1-ylamino]-3,5,6-trifluoro-4-[(2-hydroxyethyl)thio]benzenesulfonamide

PDB DOI: https://doi.org/10.2210/pdb5OHH/pdb

Classification: LYASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-07-17 Released: 2018-08-08
Deposition Author(s): Smirnov, A., Manakova, E., Grazulis, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free: 0.185
R-Value Work: 0.157
R-Value Observed: 0.159

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

Crystal structure of human carbonic anhydrase isozyme XIII with 2-[(1S)-2,3-Dihydro-1H-inden-1-ylamino]-3,5,6-trifluoro-4-[(2-hydroxyethyl)thio]benzenesulfonamide

Smirnov, A., Manakova, E., Grazulis, S., Matulis, D.

To be published.

Macromolecule Content

Total Structure Weight: 61.61 kDa
Atom Count: 5,154
Modelled Residue Count: 517
Deposited Residue Count: 526
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 13	A [auth B], B [auth A]	263	Homo sapiens	Mutation(s): 0 Gene Names: CA13 EC: 4.2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N1Q1 (Homo sapiens) Explore Q8N1Q1 Go to UniProtKB: Q8N1Q1
PHAROS: Q8N1Q1 GTEx: ENSG00000185015
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8N1Q1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5DU Query on 5DU Download Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B] mmCIF format, chain O [auth B]	O [auth B]	2-[(1S)-2,3-dihydro-1H-inden-1-ylamino]-3,5,6-trifluoro-4-[(2-hydroxyethyl)sulfanyl]benzenesulfonamide C₁₇ H₁₇ F₃ N₂ O₃ S₂ HYCVHVOZJGSFTR-NSHDSACASA-N		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain N [auth B] SDF format, chain U [auth A] SDF format, chain W [auth A] MOL2 format, chain D [auth B] MOL2 format, chain N [auth B] MOL2 format, chain U [auth A] MOL2 format, chain W [auth A] mmCIF format, chain D [auth B] mmCIF format, chain N [auth B] mmCIF format, chain U [auth A] mmCIF format, chain W [auth A]	D [auth B], N [auth B], U [auth A], W [auth A]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Focus chain N [auth B] Focus chain U [auth A] Focus chain W [auth A] Interactions & Density Focus chain D [auth B] Focus chain N [auth B] Focus chain U [auth A] Focus chain W [auth A]
BCN Query on BCN Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	BICINE C₆ H₁₃ N O₄ FSVCELGFZIQNCK-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain Q [auth A] MOL2 format, chain K [auth B] MOL2 format, chain Q [auth A] mmCIF format, chain K [auth B] mmCIF format, chain Q [auth A]	K [auth B], Q [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain Q [auth A] Interactions & Density Focus chain K [auth B] Focus chain Q [auth A]
LCP Query on LCP Download Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	PERCHLORATE ION Cl O₄ VLTRZXGMWDSKGL-UHFFFAOYSA-M		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain P [auth A] MOL2 format, chain C [auth B] MOL2 format, chain P [auth A] mmCIF format, chain C [auth B] mmCIF format, chain P [auth A]	C [auth B], P [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain P [auth A] Interactions & Density Focus chain C [auth B] Focus chain P [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A]	E [auth B] F [auth B] I [auth B] J [auth B] R [auth A] E [auth B], F [auth B], I [auth B], J [auth B], R [auth A], S [auth A], T [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain F [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Interactions & Density Focus chain E [auth B] Focus chain F [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain V [auth A] MOL2 format, chain M [auth B] MOL2 format, chain V [auth A] mmCIF format, chain M [auth B] mmCIF format, chain V [auth A]	M [auth B], V [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain M [auth B] Focus chain V [auth A] Interactions & Density Focus chain M [auth B] Focus chain V [auth A]
AZI Query on AZI Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	AZIDE ION N₃ IVRMZWNICZWHMI-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free: 0.185
R-Value Work: 0.157
R-Value Observed: 0.159
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.501	α = 90
b = 57.419	β = 90
c = 159.909	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-08-08

Deposition Author(s):

Smirnov, A.

Manakova, E.

Grazulis, S.

Revision History (Full details and data files)

Version 1.0: 2018-08-08
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description