3DA2 | pdb_00003da2

X-ray structure of human carbonic anhydrase 13 in complex with inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3DA2/pdb

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


• Deposited: 2008-05-28 Released: 2008-07-15 
• Deposition Author(s): Pilka, E.S., Picaud, S.S., Yue, W.W., King, O.N.F., Bray, J.E., Filippakopoulos, P., Roos, A.K., Pike, A.C.W., von Delft, F., Arrowsmith, C.H., Wikstrom, M., Edwards, A.M., Bountra, C., Oppermann, U., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.221 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Models: experimental

Literature

X-ray structure of human carbonic anhydrase 13 in complex with inhibitor.

Pilka, E.S., Picaud, S.S., Yue, W.W., King, O.N.F., Bray, J.E., Filippakopoulos, P., Roos, A.K., Pike, A.C.W., von Delft, F., Arrowsmith, C.H., Wikstrom, M., Edwards, A.M., Bountra, C., Oppermann, U.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 59.81 kDa 
• Atom Count: 4,573 
• Modeled Residue Count: 519 
• Deposited Residue Count: 524 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 13	A, B	262	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4MD	D [auth A], H [auth B]	N-(4-chlorobenzyl)-N-methylbenzene-1,4-disulfonamide C14 H15 Cl N2 O4 S2 IPPUTOHDQOYDIL-UHFFFAOYSA-N
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	F [auth B], G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
CL	BindingDB:  3DA2	Ki: 1.38e+8 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.221 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.637	α = 90
b = 45.138	β = 116.28
c = 87.938	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-15 
Deposition Author(s): Pilka, E.S., Picaud, S.S., Yue, W.W., King, O.N.F., Bray, J.E., Filippakopoulos, P., Roos, A.K., Pike, A.C.W., von Delft, F., Arrowsmith, C.H., Wikstrom, M., Edwards, A.M., Bountra, C., Oppermann, U., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2008-07-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description