5L70 | pdb_00005l70

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

• PDB DOI: https://doi.org/10.2210/pdb5L70/pdb

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


• Deposited: 2016-06-01 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: 2.20 Å
• R-Value Free: 
  0.238 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.177 (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.

Macromolecule Content 

• Total Structure Weight: 62.54 kDa 
• Atom Count: 4,593 
• Modeled Residue Count: 528 
• Deposited Residue Count: 532 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A, B	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	C, D	6	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth A], O [auth A], R [auth B], U [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	E [auth A], F [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], P [auth B], Q [auth B], S [auth B], T [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
4SO	BindingDB:  5L70	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: 2.20 Å
• R-Value Free:  0.238 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.21	α = 90
b = 83.37	β = 99.98
c = 79.41	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHASER	phasing

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, Structure summary
• Version 2.0: 2023-11-15
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description, Structure summary
• 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 4.0: 2024-10-02
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 4.1: 2024-11-20
  Changes: Structure summary
• Version 4.2: 2025-06-11
  Changes: Data collection, Derived calculations