5MSA | pdb_00005msa

Crystal structure of human carbonic anhydrase isozyme XII with 2,3,5,6-Tetrafluoro-4-(propylthio)benzenesulfonamide

PDB DOI: https://doi.org/10.2210/pdb5MSA/pdb

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

Deposited: 2017-01-02 Released: 2018-01-17
Deposition Author(s): Smirnov, A., Manakova, E., Grazulis, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free:
0.178 (Depositor), 0.180 (DCC)
R-Value Work:
0.141 (Depositor), 0.140 (DCC)
R-Value Observed:
0.144 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of human carbonic anhydrase isozyme XII with 2,3,5,6-Tetrafluoro-4-(propylthio)benzenesulfonamide

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

To be published.

Macromolecule Content

Total Structure Weight: 122.89 kDa
Atom Count: 10,456
Modeled Residue Count: 1,045
Deposited Residue Count: 1,052
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 12	A, B, C, D	263	Homo sapiens	Mutation(s): 0 Gene Names: CA12 EC: 4.2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for O43570 (Homo sapiens) Explore O43570 Go to UniProtKB: O43570
PHAROS: O43570 GTEx: ENSG00000074410
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O43570
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3TV Query on 3TV Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain P [auth B] SDF format, chain U [auth C] SDF format, chain Z [auth D] MOL2 format, chain F [auth A] MOL2 format, chain P [auth B] MOL2 format, chain U [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain F [auth A] mmCIF format, chain P [auth B] mmCIF format, chain U [auth C] mmCIF format, chain Z [auth D]	F [auth A], P [auth B], U [auth C], Z [auth D]	2,3,5,6-tetrafluoro-4-(propylsulfanyl)benzenesulfonamide C₉ H₉ F₄ N O₂ S₂ LKPIFWBRFVJTMY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain P [auth B] Focus chain U [auth C] Focus chain Z [auth D] Interactions & Density Focus chain F [auth A] Focus chain P [auth B] Focus chain U [auth C] Focus chain Z [auth D]
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain DA [auth D] SDF format, chain S [auth B] MOL2 format, chain BA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain S [auth B] mmCIF format, chain BA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain S [auth B]	BA [auth D], DA [auth D], S [auth B]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain DA [auth D] Focus chain S [auth B] Interactions & Density Focus chain BA [auth D] Focus chain DA [auth D] Focus chain S [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain J [auth A] SDF format, chain R [auth B] SDF format, chain W [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain R [auth B] MOL2 format, chain W [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain R [auth B] mmCIF format, chain W [auth C]	AA [auth D], J [auth A], R [auth B], W [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain J [auth A] Focus chain R [auth B] Focus chain W [auth C] Interactions & Density Focus chain AA [auth D] Focus chain J [auth A] Focus chain R [auth B] Focus chain W [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain O [auth B] SDF format, chain T [auth C] SDF format, chain Y [auth D] MOL2 format, chain E [auth A] MOL2 format, chain O [auth B] MOL2 format, chain T [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain E [auth A] mmCIF format, chain O [auth B] mmCIF format, chain T [auth C] mmCIF format, chain Y [auth D]	E [auth A], O [auth B], T [auth C], Y [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain O [auth B] Focus chain T [auth C] Focus chain Y [auth D] Interactions & Density Focus chain E [auth A] Focus chain O [auth B] Focus chain T [auth C] Focus chain Y [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain EA [auth D] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain Q [auth B] SDF format, chain V [auth C] SDF format, chain X [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain V [auth C] MOL2 format, chain X [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain V [auth C] mmCIF format, chain X [auth C]	CA [auth D] EA [auth D] G [auth A] H [auth A] I [auth A] CA [auth D], EA [auth D], G [auth A], H [auth A], I [auth A], K [auth A], L [auth A], M [auth A], N [auth A], Q [auth B], V [auth C], X [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain EA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain V [auth C] Focus chain X [auth C] Interactions & Density Focus chain CA [auth D] Focus chain EA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain V [auth C] Focus chain X [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
3TV	BindingDB: 5MSA	Kd: min: 14, max: 40 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.178 (Depositor), 0.180 (DCC)
R-Value Work: 0.141 (Depositor), 0.140 (DCC)
R-Value Observed: 0.144 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.17	α = 90
b = 74.157	β = 108.85
c = 91.559	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: 2018-01-17

Deposition Author(s):

Smirnov, A.

Manakova, E.

Grazulis, S.

Revision History (Full details and data files)

Version 1.0: 2018-01-17
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-10-09
Changes: Structure summary