5L9E | pdb_00005l9e

CRYSTAL STRUCTURE OF HUMAN CARBONIC ANHYDRASE II IN COMPLEX WITH A QUINOLINE OLIGOAMIDE FOLDAMER

• PDB DOI: https://doi.org/10.2210/pdb5L9E/pdb

• Classification: Lyase/Inhibitor
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-06-10 Released: 2017-06-21 
• Deposition Author(s): Vallade, M., Langlois d'Estaintot, B., Granier, T., Huc, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.273 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.242 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.244 (Depositor) 

Starting Model: experimental

Literature

CRYSTAL STRUCTURE OF HUMAN CARBONIC ANHYDRASE II IN COMPLEX WITH A QUINOLINE OLIGOAMIDE FOLDAMER

Vallade, M., Fischer, L., Langlois d'Estaintot, B., Granier, T., Huc, I.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 124.87 kDa 
• Atom Count: 8,501 
• Modeled Residue Count: 1,055 
• Deposited Residue Count: 1,064 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A, B, C, D	260	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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Aromatic foldamer	E, F, G, H	6	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	EA [auth C], LA [auth D], Q [auth A], Y [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	AA [auth C], BA [auth C], CA [auth C], DA [auth C], FA [auth C], GA [auth D], HA [auth D], I [auth A], IA [auth D], J [auth A], JA [auth D], K [auth A], KA [auth D], L [auth A], M [auth A], MA [auth D], N [auth A], O [auth A], P [auth A], R [auth A], S [auth A], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Z [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
4SO	BindingDB:  5L9E	Ki: min: 33, max: 260 (nM) from 6 assay(s)
		Kd: 890 (nM) from 1 assay(s)
		IC50: min: 880, max: 1.50e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.273 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.242 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.244 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.972	α = 90
b = 75.14	β = 100.08
c = 141.098	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-06-21 
Deposition Author(s): Vallade, M., Langlois d'Estaintot, B., Granier, T., Huc, I.

Revision History  

• Version 1.0: 2017-06-21
  Type: Initial release
  
• Version 1.1: 2019-06-12
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description
• Version 2.1: 2024-01-10
  Changes: Refinement description
• Version 3.0: 2024-09-04
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Other, Polymer sequence, Source and taxonomy, Structure summary
• Version 3.1: 2024-11-06
  Changes: Derived calculations, Structure summary