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- PDB-1czm: DRUG-PROTEIN INTERACTIONS: STRUCTURE OF SULFONAMIDE DRUG COMPLEXE... -

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Basic information

Entry
Database: PDB / ID: 1czm
TitleDRUG-PROTEIN INTERACTIONS: STRUCTURE OF SULFONAMIDE DRUG COMPLEXED WITH HUMAN CARBONIC ANHYDRASE I
ComponentsCARBONIC ANHYDRASE ICarbonic anhydrase
KeywordsLYASE(OXO-ACID) / PROTEIN-DRUG INTERACTIONS / OXO-ACID LYASE / SULFONAMIDES
Function / homology
Function and homology information


hydro-lyase activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen ...hydro-lyase activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / one-carbon metabolic process / extracellular exosome / zinc ion binding / 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
3-ACTOXYMERCURI-4-AMINOBENZENESULFONAMIDE / : / Carbonic anhydrase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsChakravarty, S. / Kannan, K.K.
Citation
Journal: J.Mol.Biol. / Year: 1994
Title: Drug-protein interactions. Refined structures of three sulfonamide drug complexes of human carbonic anhydrase I enzyme.
Authors: Chakravarty, S. / Kannan, K.K.
#1: Journal: J.Biosci. / Year: 1985
Title: Drug Protein Interaction at the Molecular Level: A Study of Sulphonamide Carbonic Anhydrase Complexes
Authors: Chakravarty, S. / Yadava, V.S. / Kumar, V. / Kannan, K.K.
#2: Journal: Drug Action at the Molecular Level / Year: 1977
Title: Structure and Function of Carbonic Anhydrase: Comparative Studies of Sulphonamide Binding to Human Erythrocyte Carbonic Anhydrases B and C
Authors: Kannan, K.K. / Vaara, I. / Notstrand, B. / Lovgren, S. / Borell, A. / Fridborg, K. / Petef, M.
History
DepositionNov 28, 1993Processing site: BNL
Revision 1.0Apr 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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 7, 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_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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET SHEET B1 OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET ...SHEET SHEET B1 OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS *B1A* AND *B1B* ARE DEFINED. STRANDS 5, 6, 7, 8, 9, AND 10 OF B1A ARE IDENTICAL TO STRANDS 2, 3, 4, 5, 6, AND 7 OF B1B, RESPECTIVELY.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CARBONIC ANHYDRASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2748
Polymers28,7751
Non-polymers1,4997
Water3,207178
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.850, 75.310, 37.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO 30 / 2: CIS PROLINE - PRO 202
3: THE SULFONAMIDE DRUG MOLECULE 3-ACETOXYMERCURI-4-AMINOBENZENE SULFONAMIDE (AMSULF/AMS) HAS BEEN ASSIGNED THE THREE LETTER CODE AAS IN THE COORDINATE FILE. NO ELECTRON DENSITY OBTAINED FOR THE ...3: THE SULFONAMIDE DRUG MOLECULE 3-ACETOXYMERCURI-4-AMINOBENZENE SULFONAMIDE (AMSULF/AMS) HAS BEEN ASSIGNED THE THREE LETTER CODE AAS IN THE COORDINATE FILE. NO ELECTRON DENSITY OBTAINED FOR THE MERCURIC ACETATE PART OF AMSULF IN THE ACTIVE SITE UNLIKE THE REPORTED CASE OF ISOZYME HCAII-AMSULF COMPLEX (A.E.ERIKSSON, DOCTORAL THESIS, UPSAALA, SWEDEN, 1988).
4: THE DRUG MOLECULE HAS WELL DEFINED ELECTRON DENSITY IN THE ACTIVE SITE OF THE ENZYME. WHEN THE DRUG BINDS TO THE ENZYME, HIS 200 IN THE LOOP REGION UNDERGOES A SIGNIFICANT CHANGE AS COMPARED TO THE NATIVE STRUCTURE.
5: ACTIVE SITE HYDROGEN BONDED SOLVENT NETWORK INVOLVING HIS 67 AND HIS 200 IS POSSIBLY IMPORTANT FOR THE CATALYTIC ACTIVITY AND INHIBITION OF THIS ISOENZYME. SEE ALSO FTNOTE 4.
6: ZINC ZN(II) IS THE CATALYTICALLY ESSENTIALL ZINC ION.
7: RESIDUES HG 266 AND HG 267 ARE THE TWO DISORDERED MERCURY SITES LOCATED NEAR RESIDUE CYS 212 WHICH ALSO SHOWS CONFORMATIONAL DISORDER IN THE (FO-FC) ELECTRON DENSITY MAP.
8: RESIDUES HG 264 AND HG 265 ARE TWO NEW MERCURY SITES NEAR RESIDUES 185-189.
9: ASSIGNMENT OF HG 269 NEAR LEU 147 IS TENTATIVELY BASED ON HEAVY ELECTRON DENSITY APPEARING IN THE (F0-FC) MAP. THE POSSIBILITY OF SOME OTHER IMPURITY GROUP CANNOT BE RULED OUT.

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Components

#1: Protein CARBONIC ANHYDRASE I / Carbonic anhydrase


Mass: 28774.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P00915, 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 / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Hg
#4: Chemical ChemComp-AAS / 3-ACTOXYMERCURI-4-AMINOBENZENESULFONAMIDE


Mass: 430.831 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10HgN2O4S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE DRUG MOLECULE HAS WELL DEFINED ELECTRON DENSITY IN THE ACTIVE SITE OF THE ENZYME. WHEN THE DRUG ...THE DRUG MOLECULE HAS WELL DEFINED ELECTRON DENSITY IN THE ACTIVE SITE OF THE ENZYME. WHEN THE DRUG BINDS TO THE ENZYME, HIS 200 IN THE LOOP REGION UNDERGOES A SIGNIFICANT CHANGE AS COMPARED TO THE NATIVE STRUCTURE. ACTIVE SITE HYDROGEN BONDED SOLVENT NETWORK INVOLVING HIS 67 AND HIS 200 IS POSSIBLY IMPORTANT FOR THE CATALYTIC ACTIVITY AND INHIBITION OF THIS ISOENZYME.
Nonpolymer detailsZINC ZN(II) IS THE CATALYTICALLY ESSENTIALL ZINC ION. THE SULFONAMIDE DRUG MOLECULE 3- ...ZINC ZN(II) IS THE CATALYTICALLY ESSENTIALL ZINC ION. THE SULFONAMIDE DRUG MOLECULE 3-ACETOXYMERCURI-4-AMINOBENZENE SULFONAMIDE (AMSULF/AMS) HAS BEEN ASSIGNED THE THREE LETTER CODE AAS IN THE COORDINATE FILE. NO ELECTRON DENSITY OBTAINED FOR THE MERCURIC ACETATE PART OF AMSULF IN THE ACTIVE SITE UNLIKE THE REPORTED CASE OF ISOZYME HCAII-AMSULF COMPLEX (A.E.ERIKSSON, DOCTORAL THESIS, UPSAALA, SWEDEN, 1988).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.14 %
Crystal grow
*PLUS
Method: unknown

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Processing

SoftwareName: PROTEIN / Classification: refinement
RefinementResolution: 2→8 Å
Details: ALTHOUGH HYDROGEN ATOMS ARE BEING LISTED IN THE COMPLETE FORMULAE OF HET GROUPS, THEY ARE NOT PRESENT IN THE ACTUAL COORDINATE SET. ME2 IS DIVALENT MERCURY. RESIDUE SER 2 AND WATER MOLECULES ...Details: ALTHOUGH HYDROGEN ATOMS ARE BEING LISTED IN THE COMPLETE FORMULAE OF HET GROUPS, THEY ARE NOT PRESENT IN THE ACTUAL COORDINATE SET. ME2 IS DIVALENT MERCURY. RESIDUE SER 2 AND WATER MOLECULES 399 AND 435 SHOULD BE TREATED WITH CAUTION. RESIDUES HG 266 AND HG 267 ARE THE TWO DISORDERED MERCURY SITES LOCATED NEAR RESIDUE CYS 212 WHICH ALSO SHOWS CONFORMATIONAL DISORDER IN THE (FO-FC) ELECTRON DENSITY MAP. ASSIGNMENT OF HG 269 NEAR LEU 147 IS TENTATIVELY BASED ON HEAVY ELECTRON DENSITY APPEARING IN THE (F0-FC) MAP. THE POSSIBILITY OF SOME OTHER IMPURITY GROUP CANNOT BE RULED OUT.
RfactorNum. reflection
obs0.186 13169
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2034 0 17 178 2229
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.02
X-RAY DIFFRACTIONp_angle_d0.0370.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0480.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor22
X-RAY DIFFRACTIONp_staggered_tor19.219.2
X-RAY DIFFRACTIONp_orthonormal_tor31.831.8
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Rfactor obs: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS

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