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- PDB-1hcb: ENZYME-SUBSTRATE INTERACTIONS: STRUCTURE OF HUMAN CARBONIC ANHYDR... -

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Basic information

Entry
Database: PDB / ID: 1hcb
TitleENZYME-SUBSTRATE INTERACTIONS: STRUCTURE OF HUMAN CARBONIC ANHYDRASE I COMPLEXED WITH BICARBONATE
ComponentsCARBONIC ANHYDRASE I
KeywordsLYASE(OXO-ACID)
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
BICARBONATE ION / Carbonic anhydrase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsKumar, V. / Kannan, K.K.
Citation
Journal: J.Mol.Biol. / Year: 1994
Title: Enzyme-substrate interactions. Structure of human carbonic anhydrase I complexed with bicarbonate.
Authors: Kumar, V. / Kannan, K.K.
#1: Journal: Acta Crystallogr.,Sect.A / Year: 1993
Title: Structure of Human Carbonic Anhydrase I Complexed with Gold Cyanide Inhibitor: Inhibition Mechanism
Authors: Kumar, V. / Kannan, K.K.
#2: Journal: Acta Crystallogr.,Sect.A / Year: 1987
Title: Human Carbonic Anhydrase I-Iodide Complex: Structure and Inhibition Mechanism
Authors: Kumar, V. / Satyamurthy, P. / Kannan, K.K.
History
DepositionJan 7, 1994Processing 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.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 THIS STRUCTURE CONTAINS A BIFURCATED SHEET. THIS IS REPRESENTED BY PRESENTING TWO SHEETS ON ...SHEET THIS STRUCTURE CONTAINS A BIFURCATED SHEET. THIS IS REPRESENTED BY PRESENTING TWO SHEETS ON *SHEET* RECORDS BELOW. STRAND 5 IS DIFFERENT IN SHEETS S1A AND S1B.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CARBONIC ANHYDRASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9013
Polymers28,7751
Non-polymers1262
Water4,576254
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

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Components

#1: Protein CARBONIC ANHYDRASE I


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-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsATOM O HOH 520 (PARTIAL OCCUPANCY) MAKES SHORT CONTACT WITH 522 HCO GROUP AND MAY BE THE PARTIALLY ...ATOM O HOH 520 (PARTIAL OCCUPANCY) MAKES SHORT CONTACT WITH 522 HCO GROUP AND MAY BE THE PARTIALLY OVERLAPPING BINDING SITE OF THE HET 522 HCO GROUP. HOH 521 O ATOM IS PARTIALLY OCCUPIED SOLVENT, OVERLAPPING WITH O1 ATOM OF 522 HCO GROUP. HET ATOM ZN2 IS ESSENTIAL METAL ION. HET RESIDUE HCO IS BICARBONATE ANION, SUBSTRATE FOR THE REVERSE REACTION CATALYZED BY CARBONIC ANHYDRASE ISOENZYMES.
Sequence detailsON THE BASIS OF THE PRESENT COMPLEX STRUCTURE THE FOLLOWING SEQUENCE MODIFICATION IN THE NATIVE ...ON THE BASIS OF THE PRESENT COMPLEX STRUCTURE THE FOLLOWING SEQUENCE MODIFICATION IN THE NATIVE HUMAN CARBONIC ANHYDRASE ATOMIC MODEL (PDB IDENT CODE 2CAB, VERSION OF 10/84) HAVE BEEN MADE IN THE SUBMITTED ATOMIC MODEL. SEQUENCE NUMBER 74 75 RESIDUE TYPE ASP ASN THESE CHANGES ARE CONSISTENT WITH THE KNOWN CHEMICAL SEQUENCE OF HUMAN CARBONIC ANHYDRASE I ENZYME.

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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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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.6 Å / Num. obs: 24976 / % possible obs: 79.1 % / Rmerge(I) obs: 0.0817

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.6→10 Å
Details: THE SIDE CHAINS OF RESIDUES ASP 4, ASP 9, LYS 10, LEU 19 AND LYS149 SHOW VERY POOR ELECTRON DENSITY IN THE FOURIER MAPS.
RfactorNum. reflection
obs0.177 24976
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2023 0 5 254 2282
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
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_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 10 Å / Num. reflection obs: 24976 / Rfactor obs: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS

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