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- PDB-5l6t: CRYSTAL STRUCTURE OF HUMAN CARBONIC ANHYDRASE II IN COMPLEX WITH ... -

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Entry
Database: PDB / ID: 5l6t
TitleCRYSTAL STRUCTURE OF HUMAN CARBONIC ANHYDRASE II IN COMPLEX WITH A QUINOLINE OLIGOAMIDE FOLDAMER
ComponentsCarbonic anhydrase 2
KeywordsLyase/Inhibitor / PROTEIN-FOLDAMER COMPLEX / PROTEIN FOLDAMER INTERACTIONS / MODIFIED INHIBITOR / ANCHORED FOLDAMER / HCAII DIMERISATION / QUINOLINE OLIGOAMIDE FOLDAMER / BENZENE SULFONAMIDE MODIFIED INHIBITOR / LYASE-INHIBITOR COMPLEX
Function / homology
Function and homology information


positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / morphogenesis of an epithelium / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / neuron cellular homeostasis / one-carbon metabolic process / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Carbonic Anhydrase II / Alpha carbonic anhydrase / Carbonic anhydrase, alpha-class, conserved site / Alpha-carbonic anhydrases signature. / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase ...Carbonic Anhydrase II / Alpha carbonic anhydrase / Carbonic anhydrase, alpha-class, conserved site / Alpha-carbonic anhydrases signature. / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-6H0 / Chem-QCL / Chem-QUK / Chem-QVE / 8-azanyl-4-oxidanyl-quinoline-2-carboxylic acid / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsVallade, M. / Langlois d'Estaintot, B. / Granier, T. / Huc, I.
CitationJournal: To Be Published
Title: CRYSTAL STRUCTURE OF HUMAN CARBONIC ANHYDRASE II IN COMPLEX WITH A QUINOLINE OLIGOAMIDE FOLDAMER
Authors: Vallade, M. / Fischer, L. / Langlois d'Estaintot, B. / Granier, T. / Huc, I.
History
DepositionMay 31, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name / _citation_author.name
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_ncs_dom_lim / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_asym.entity_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues
Revision 2.1Jan 10, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase 2
B: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,73931
Polymers58,5782
Non-polymers4,16029
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-331 kcal/mol
Surface area22180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.490, 83.810, 79.850
Angle α, β, γ (deg.)90.000, 99.980, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 0 / Auth seq-ID: 4 - 259 / Label seq-ID: 4 - 259

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Carbonic anhydrase 2 / / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II


Mass: 29289.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pet11d / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 8 types, 206 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-6H0 / ~{N}-[[3-(4-formamidobutoxy)phenyl]methyl]-4-sulfamoyl-benzamide


Mass: 405.468 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H23N3O5S
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-QVS / 8-azanyl-4-oxidanyl-quinoline-2-carboxylic acid


Mass: 204.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H8N2O3
#6: Chemical ChemComp-QUK / 8-azanyl-4-(3-azanylpropoxy)quinoline-2-carboxylic acid


Mass: 261.276 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H15N3O3
#7: Chemical ChemComp-QVE / 8-azanyl-4-(2-hydroxy-2-oxoethyloxy)quinoline-2-carboxylic acid


Mass: 262.218 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H10N2O5
#8: Chemical ChemComp-QCL / 8-azanyl-4-(2-ethylbutoxy)quinoline-2-carbaldehyde


Mass: 272.342 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H20N2O2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9 / Details: ZnOAc 0.2M NaCac 0.1 M PEG 8000 pH 7.1 NaN3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 18, 2015 / Details: Kirkpatrick-Baez (KB) mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.212→78.642 Å / Num. obs: 15030 / % possible obs: 89.8 % / Redundancy: 2.5 % / Biso Wilson estimate: 33.223 Å2 / Rsym value: 0.138 / Net I/av σ(I): 4.161 / Net I/σ(I): 4.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.65-2.792.50.4121.8192.3
2.79-2.962.50.32.4192
2.96-3.172.50.223.1191.7
3.17-3.422.50.1694190.9
3.42-3.752.50.134.9190.8
3.75-4.192.50.115.4190.2
4.19-4.842.50.1095.1187.2
4.84-5.932.50.1095.3185.1
5.93-8.382.50.0787.1181
8.38-83.812.50.0737185.5

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.22data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
PHASER6.5.015phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2KS3

2ks3
PDB Unreleased entry


Resolution: 2.65→78.64 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.833 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.435
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2782 750 5 %RANDOM
Rwork0.2204 ---
obs0.2233 14263 88.88 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 82.91 Å2 / Biso mean: 40.455 Å2 / Biso min: 12.18 Å2
Baniso -1Baniso -2Baniso -3
1--2.01 Å20 Å21.52 Å2
2--0.24 Å2-0 Å2
3---1.17 Å2
Refinement stepCycle: final / Resolution: 2.65→78.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4011 0 237 177 4425
Biso mean--35.43 31.13 -
Num. residues----509
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.024415
X-RAY DIFFRACTIONr_bond_other_d0.0020.023991
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.9915967
X-RAY DIFFRACTIONr_angle_other_deg3.9563.0089143
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5485507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.95824.503191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.75515654
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8131514
X-RAY DIFFRACTIONr_chiral_restr0.0860.2599
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0214943
X-RAY DIFFRACTIONr_gen_planes_other0.0130.021028
X-RAY DIFFRACTIONr_mcbond_it0.361.5942048
X-RAY DIFFRACTIONr_mcbond_other0.3571.5952040
X-RAY DIFFRACTIONr_mcangle_it0.6232.3912542
Refine LS restraints NCS

Ens-ID: 1 / Number: 29208 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 60 -
Rwork0.281 1087 -
all-1147 -
obs--93.03 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2117-0.06840.66872.5646-0.07223.8870.0085-0.0250.0594-0.1153-0.07430.11310.111-0.11810.06570.2123-0.0281-0.07510.01270.00510.032841.33213.07432.388
23.5427-0.46340.79553.49470.45444.31830.0269-0.23420.04680.1948-0.17030.35640.2723-0.19490.14340.2531-0.0199-0.04270.1760.01520.072554.25721.50468.811
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 260
2X-RAY DIFFRACTION1A300 - 301
3X-RAY DIFFRACTION1B302 - 305
4X-RAY DIFFRACTION1C1 - 4
5X-RAY DIFFRACTION1C6
6X-RAY DIFFRACTION1C8
7X-RAY DIFFRACTION2B4 - 259
8X-RAY DIFFRACTION2C5
9X-RAY DIFFRACTION2C9
10X-RAY DIFFRACTION2C11 - 12
11X-RAY DIFFRACTION2B300 - 301
12X-RAY DIFFRACTION2A302 - 305

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