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- PDB-1ydd: STRUCTURAL BASIS OF INHIBITOR AFFINITY TO VARIANTS OF HUMAN CARBO... -

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Basic information

Entry
Database: PDB / ID: 1ydd
TitleSTRUCTURAL BASIS OF INHIBITOR AFFINITY TO VARIANTS OF HUMAN CARBONIC ANHYDRASE II
ComponentsCARBONIC ANHYDRASE II
KeywordsHYDRO-LYASE
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 activity / cyanamide hydratase / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase activity / cyanamide hydratase / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / angiotensin-activated signaling pathway / regulation of intracellular pH / positive regulation of synaptic transmission, GABAergic / 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 / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytoplasm / cytosol
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
5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE / : / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsNair, S.K. / Christianson, D.W.
CitationJournal: Biochemistry / Year: 1995
Title: Structural basis of inhibitor affinity to variants of human carbonic anhydrase II.
Authors: Nair, S.K. / Krebs, J.F. / Christianson, D.W. / Fierke, C.A.
History
DepositionDec 22, 1994Processing site: BNL
Revision 1.0Feb 14, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.value / _struct_conn.pdbx_dist_value / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CARBONIC ANHYDRASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6904
Polymers29,2021
Non-polymers4883
Water1,820101
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.700, 41.700, 73.000
Angle α, β, γ (deg.)90.00, 104.60, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO 30 / 2: CIS PROLINE - PRO 202

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Components

#1: Protein CARBONIC ANHYDRASE II


Mass: 29201.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P00918, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#4: Chemical ChemComp-AZM / 5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE


Mass: 222.245 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6N4O3S2 / Comment: medication*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Compound detailsSECONDARY STRUCTURE ELEMENTS WERE DEFINED USING THE PROGRAM *DSSP* (W. KABSCH, C. SANDER, ...SECONDARY STRUCTURE ELEMENTS WERE DEFINED USING THE PROGRAM *DSSP* (W. KABSCH, C. SANDER, BIOPOLYMERS, V. 22, P. 2577, 1983).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.86 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, sitting drop / Details: Nair, S. K., (1993) Biochemistry, 32, 4506.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.3 mMenzyme1drop
250 mMTris-HCl1drop
33 mM1dropNaN3
450 mMTris-HCl1reservoir
53 mM1reservoirNaN3
61.75-2.5 Mammonium sulfate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 11425 / Num. measured all: 20609 / Rmerge(I) obs: 0.093

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.1→6.5 Å / σ(I): 2 /
RfactorNum. reflection
obs0.187 9724
Refinement stepCycle: LAST / Resolution: 2.1→6.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 15 101 2158
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.03
X-RAY DIFFRACTIONp_angle_d0.0260.05
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0310.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.3761
X-RAY DIFFRACTIONp_mcangle_it0.6661.5
X-RAY DIFFRACTIONp_scbond_it0.2891
X-RAY DIFFRACTIONp_scangle_it0.5171.5
X-RAY DIFFRACTIONp_plane_restr0.010.025
X-RAY DIFFRACTIONp_chiral_restr0.0960.15
X-RAY DIFFRACTIONp_singtor_nbd0.1850.5
X-RAY DIFFRACTIONp_multtor_nbd0.2460.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.260.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor15.620
X-RAY DIFFRACTIONp_staggered_tor17.220
X-RAY DIFFRACTIONp_orthonormal_tor26.820
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_dihedral_angle_d1.36
X-RAY DIFFRACTIONp_dihedral_angle_deg

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