3IAI

Crystal structure of the catalytic domain of the tumor-associated human carbonic anhydrase IX

PDB DOI: https://doi.org/10.2210/pdb3IAI/pdb

Classification: LYASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2009-07-14 Released: 2009-09-08
Deposition Author(s): Alterio, V., Di Fiore, A., De Simone, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.181
R-Value Work: 0.157

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 120.75 kDa
Atom Count: 10,134
Modelled Residue Count: 1,014
Deposited Residue Count: 1,028
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 9	A, B, C, D	257	Homo sapiens	Mutation(s): 1 Gene Names: CA9, G250, MN EC: 4.2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16790 (Homo sapiens) Explore Q16790 Go to UniProtKB: Q16790
PHAROS: Q16790 GTEx: ENSG00000107159
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q16790
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, G, H	5		N-Glycosylation	Interactions Focus chain E Focus chain F Focus chain G Focus chain H Interactions & Density Focus chain E Focus chain F Focus chain G Focus chain H
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AZM Query on AZM Download Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain J [auth A] SDF format, chain OA [auth D] SDF format, chain V [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain V [auth B]	FA [auth C], J [auth A], OA [auth D], V [auth B]	5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE C₄ H₆ N₄ O₃ S₂ BZKPWHYZMXOIDC-UHFFFAOYSA-N		Interactions Focus chain FA [auth C] Focus chain J [auth A] Focus chain OA [auth D] Focus chain V [auth B] Interactions & Density Focus chain FA [auth C] Focus chain J [auth A] Focus chain OA [auth D] Focus chain V [auth B]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain LA [auth C] SDF format, chain R [auth A] SDF format, chain WA [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain LA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain WA [auth D]	CA [auth B], LA [auth C], R [auth A], WA [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain CA [auth B] Focus chain LA [auth C] Focus chain R [auth A] Focus chain WA [auth D] Interactions & Density Focus chain CA [auth B] Focus chain LA [auth C] Focus chain R [auth A] Focus chain WA [auth D]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain DA [auth B] SDF format, chain MA [auth C] SDF format, chain S [auth A] SDF format, chain XA [auth D] MOL2 format, chain T [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain MA [auth C] MOL2 format, chain S [auth A] MOL2 format, chain XA [auth D]	DA [auth B], MA [auth C], S [auth A], T [auth A], XA [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain DA [auth B] Focus chain MA [auth C] Focus chain S [auth A] Focus chain T [auth A] Focus chain XA [auth D] Interactions & Density Focus chain DA [auth B] Focus chain MA [auth C] Focus chain S [auth A] Focus chain T [auth A] Focus chain XA [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain HA [auth C] SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain GA [auth C] SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain PA [auth D] SDF format, chain Q [auth A] SDF format, chain QA [auth D] SDF format, chain RA [auth D] SDF format, chain SA [auth D] SDF format, chain TA [auth D] SDF format, chain UA [auth D] SDF format, chain VA [auth D] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain HA [auth C] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain RA [auth D] MOL2 format, chain SA [auth D] MOL2 format, chain TA [auth D] MOL2 format, chain UA [auth D] MOL2 format, chain VA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B]	AA [auth B] BA [auth B] GA [auth C] HA [auth C] IA [auth C] AA [auth B], BA [auth B], GA [auth C], HA [auth C], IA [auth C], JA [auth C], K [auth A], KA [auth C], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], PA [auth D], Q [auth A], QA [auth D], RA [auth D], SA [auth D], TA [auth D], UA [auth D], VA [auth D], W [auth B], X [auth B], Y [auth B], Z [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain TA [auth D] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain TA [auth D] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain U [auth B] SDF format, chain I [auth A] SDF format, chain NA [auth D] MOL2 format, chain EA [auth C] MOL2 format, chain U [auth B] MOL2 format, chain I [auth A] MOL2 format, chain NA [auth D]	EA [auth C], I [auth A], NA [auth D], U [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain I [auth A] Focus chain NA [auth D] Focus chain U [auth B] Interactions & Density Focus chain EA [auth C] Focus chain I [auth A] Focus chain NA [auth D] Focus chain U [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
AZM	BindingDB: 3IAI	Ki: min: 0.06, max: 30 (nM) from 12 assay(s)
		Kd: min: 0.03, max: 50 (nM) from 12 assay(s)
		IC50: min: 2.6, max: 2134 (nM) from 61 assay(s)
PO4	BindingDB: 3IAI	Ki: 5.60e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.181
R-Value Work: 0.157
Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.18	α = 90
b = 144.18	β = 90
c = 208.89	γ = 120

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-09-08

Deposition Author(s):

Alterio, V.

Di Fiore, A.

De Simone, G.

Revision History (Full details and data files)

Version 1.0: 2009-09-08
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2021-10-13
Changes: Database references, Structure summary
Version 2.2: 2023-09-06
Changes: Data collection, Refinement description