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- PDB-5jn8: Crystal Structure for the complex of human carbonic anhydrase IV ... -

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Basic information

Entry
Database: PDB / ID: 5jn8
TitleCrystal Structure for the complex of human carbonic anhydrase IV and acetazolamide
ComponentsCarbonic anhydrase 4
Keywordslyase/lyase inhibitor / Carbonic anhydrase / Lyase / Inhibitor binding / lyase-lyase inhibitor complex
Function / homology
Function and homology information


bicarbonate transport / transport vesicle membrane / endoplasmic reticulum-Golgi intermediate compartment / rough endoplasmic reticulum / secretory granule membrane / Reversible hydration of carbon dioxide / brush border membrane / carbonic anhydrase / carbonate dehydratase activity / trans-Golgi network ...bicarbonate transport / transport vesicle membrane / endoplasmic reticulum-Golgi intermediate compartment / rough endoplasmic reticulum / secretory granule membrane / Reversible hydration of carbon dioxide / brush border membrane / carbonic anhydrase / carbonate dehydratase activity / trans-Golgi network / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / one-carbon metabolic process / apical plasma membrane / external side of plasma membrane / perinuclear region of cytoplasm / Golgi apparatus / cell surface / extracellular exosome / zinc ion binding / membrane / plasma membrane
Similarity search - Function
Carbonic anhydrase, CA4/CA15 / 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. ...Carbonic anhydrase, CA4/CA15 / 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
ACETATE ION / 5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE / Carbonic anhydrase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsChen, Z. / Waheed, A. / Di Cera, E. / Sly, W.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) United States
Citation
Journal: Eur. Biophys. J. / Year: 2018
Title: Intrinsic thermodynamics of high affinity inhibitor binding to recombinant human carbonic anhydrase IV.
Authors: Mickeviciute, A. / Timm, D.D. / Gedgaudas, M. / Linkuviene, V. / Chen, Z. / Waheed, A. / Michailoviene, V. / Zubriene, A. / Smirnov, A. / Capkauskaite, E. / Baranauskiene, L. / Jachno, J. / ...Authors: Mickeviciute, A. / Timm, D.D. / Gedgaudas, M. / Linkuviene, V. / Chen, Z. / Waheed, A. / Michailoviene, V. / Zubriene, A. / Smirnov, A. / Capkauskaite, E. / Baranauskiene, L. / Jachno, J. / Revuckiene, J. / Manakova, E. / Grazulis, S. / Matuliene, J. / Di Cera, E. / Sly, W.S. / Matulis, D.
#1: Journal: PNAS / Year: 1996
Title: Crystal structure of the Secretory form of membrane-associated human carbonic anhydrase IV at 2.8-A resolution
Authors: Stams, T. / Nair, S.K. / Qkuyama, T. / Waheed, A. / Sly, W.S. / Christianson, D.W.
History
DepositionApr 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software
Item: _pdbx_audit_support.funding_organization / _software.classification
Revision 1.2Feb 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 4
B: Carbonic anhydrase 4
C: Carbonic anhydrase 4
D: Carbonic anhydrase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,51734
Polymers121,4584
Non-polymers3,05930
Water17,330962
1
A: Carbonic anhydrase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,24710
Polymers30,3641
Non-polymers8829
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Carbonic anhydrase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,28010
Polymers30,3641
Non-polymers9159
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Carbonic anhydrase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0878
Polymers30,3641
Non-polymers7237
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Carbonic anhydrase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9036
Polymers30,3641
Non-polymers5395
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.933, 123.471, 151.237
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Carbonic anhydrase 4 / / Carbonate dehydratase IV / Carbonic anhydrase IV / CA-IV


Mass: 30364.473 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA4 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P22748, carbonic anhydrase

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Non-polymers , 6 types, 992 molecules

#2: Chemical
ChemComp-AZM / 5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE / Acetazolamide


Mass: 222.245 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6N4O3S2 / Comment: medication*YM
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 962 / 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: 2.5 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 100 mM Na acetate, 200 mM AmSO4 and 21% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 2, 2015
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→95.64 Å / Num. obs: 102801 / % possible obs: 98.5 % / Observed criterion σ(F): -0.5 / Observed criterion σ(I): -0.5 / Redundancy: 4.5 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 10.2
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 2 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1ZNC
Resolution: 1.85→95.64 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.497 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22805 5127 5 %RANDOM
Rwork0.18473 ---
obs0.18688 97258 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.215 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.85→95.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8360 0 166 962 9488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0228738
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.97211810
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25251031
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.57424.889405
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.238151555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9621537
X-RAY DIFFRACTIONr_chiral_restr0.0850.21251
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216519
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3761.55214
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.72428419
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.40833524
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3684.53387
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 373 -
Rwork0.302 6892 -
obs--95.43 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.943-0.8516-0.52754.15251.2675.42230.0151-0.0248-0.46390.21140.1335-0.20080.42570.2417-0.14870.14310.005-0.01320.15730.01810.187938.7682-6.898116.8039
24.6846-1.3837-0.61892.61410.62442.3302-0.067-0.6212-0.13210.35220.09690.2686-0.0117-0.0785-0.030.1849-0.04370.03710.12010.02720.101722.77256.496726.9206
32.5062-1.9955-1.17923.41981.64771.45410.004-0.02820.4136-0.11880.0859-0.2067-0.28370.1279-0.08980.1485-0.0398-0.04420.18310.00770.134432.799521.405512.333
41.6596-0.6736-0.10465.22312.92723.3832-0.0506-0.07030.17730.0390.1345-0.2668-0.1050.2337-0.08390.0832-0.0269-0.01880.08310.03660.059732.299617.15515.6415
56.93953.2483-4.42192.5306-0.34886.1078-0.2990.63560.119-0.12990.25030.19110.5471-0.42620.04870.32110.04-0.09090.0785-0.00310.127919.56183.802313.6809
63.23442.23031.46756.15434.06255.16020.067-0.20660.04230.3545-0.0052-0.13520.0550.0711-0.06180.07950.00680.01710.06560.03120.069630.027515.950320.8814
75.15370.30370.90881.77730.31751.52990.07220.16670.353-0.1684-0.0806-0.0481-0.16960.15570.00840.1864-0.01940.02190.15220.00370.068834.48913.3086-0.3586
85.26911.3505-4.96161.6265-1.97468.62510.09890.69740.3663-0.2580.10580.3737-0.491-0.828-0.20480.21830.0222-0.03360.1395-0.01160.198521.295622.225912.052
91.1641-0.7441-0.95311.55820.92573.57730.02310.0408-0.0352-0.0141-0.02540.00420.05660.11390.00230.0426-0.0394-0.00990.05870.01130.087231.33256.31710.4901
102.2611-3.9041-1.78568.12851.78045.339-0.2856-0.2617-0.4040.52890.16110.86730.3146-0.05820.12450.0657-0.01570.03360.19990.0260.130420.99176.339225.9297
110.9558-0.22573.57166.30342.969315.798-0.24420.20490.13670.09410.3624-0.9412-0.98771.1245-0.11820.1454-0.09440.00820.2437-0.0540.239635.65535.6478-21.2567
122.70161.5637-0.78393.8192-0.90012.6485-0.12460.4590.0181-0.27190.12980.12440.1259-0.0999-0.00530.11530.0207-0.04840.0958-0.02090.081723.6902-5.2979-30.73
136.5181-2.03542.25515.4114-0.77263.15630.10040.1907-0.6785-0.12770.01940.35360.32050.0853-0.11970.2123-0.01930.06190.1213-0.01010.165921.0312-25.924-20.7255
141.4411.68170.98734.01562.15091.1779-0.06190.1501-0.36060.04590.2372-0.32790.05450.1751-0.17530.23730.06250.0250.16520.02810.202735.8721-19.7668-18.2746
151.35270.91071.22991.92760.10661.53730.016-0.0746-0.00160.1230.01930.07290.0112-0.088-0.03540.14290.03220.00890.06520.01660.067825.8729-11.4397-17.4456
162.3742-0.16190.24843.40392.03725.12280.03980.0198-0.0687-0.0862-0.0220.08790.1047-0.0632-0.01790.0917-0.0054-0.03670.00120.00090.222626.6663-17.7674-18.2056
173.07530.84682.43421.8047-0.04854.02190.1776-0.3015-0.27550.2248-0.1104-0.00870.345-0.0575-0.06720.14820.05530.01570.1-0.00750.150730.4074-16.4071-13.5845
182.01062.07612.53112.76130.93947.83860.1286-0.4290.08080.0881-0.33940.06920.4507-0.84890.21080.14580.00420.01090.1366-0.03770.15822.7406-13.9251-14.5777
194.69471.26980.08041.9544-0.73033.6055-0.0296-0.056-0.003-0.0165-0.0201-0.11710.06210.15940.04960.09150.026-0.02690.0522-0.01870.049936.0531-2.9918-7.2779
202.29241.17941.75532.71231.14153.439-0.17880.04190.2031-0.1677-0.02070.301-0.2751-0.04780.19950.06070.02590.02130.0792-0.0050.112824.5205-4.8762-22.6706
217.1256-0.5444-2.59031.998-4.472612.17960.3478-0.16220.82290.3005-0.3581-0.2386-0.95331.06740.01030.216-0.12990.04150.2502-0.080.31920.408720.9556-18.0555
224.15141.50210.95543.27710.85951.78230.0837-0.3644-0.41110.2846-0.08240.17460.2142-0.1938-0.00130.12810.00950.03170.14190.03990.14212.69993.9091-11.4695
233.06070.0629-1.48220.8023-0.36791.9101-0.03640.0605-0.00120.00630.00880.278-0.1275-0.27750.02760.12380.0214-0.00840.1274-0.04270.1249-4.004617.7806-24.1101
243.1-0.3107-1.471.561-0.60693.46570.25180.0140.06790.0455-0.11010.0729-0.0938-0.2214-0.14170.0648-0.0336-0.02240.073-0.01940.1006-0.971910.6453-17.6968
2519.0035-3.6891-16.39620.72653.395624.39010.1613-0.6187-0.11770.00740.09930.0167-0.11150.2584-0.26060.2651-0.06910.04890.2094-0.0240.202-7.561913.807-2.1755
262.09491.6307-0.41732.3241-1.62487.6686-0.19620.4536-0.3311-0.4410.061-0.03140.4797-0.61990.13520.10090.0303-0.01940.3192-0.15480.19-0.222511.6214-32.8461
274.62422.853-0.33185.3013-1.17582.8226-0.20460.39120.0262-0.4960.23850.34210.0708-0.3186-0.03390.13640.0729-0.01230.1954-0.03830.106-1.753520.1656-32.9117
281.93312.6738-4.5054.1985-4.923814.061-0.41010.44030.0452-0.4680.56030.20660.9882-0.9666-0.15020.1273-0.027-0.16840.153-0.13730.9943-7.20430.4878-21.4292
292.52671.0381-1.45951.4706-1.42874.2348-0.02130.0964-0.0399-0.03970.0360.05530.004-0.1865-0.01480.02770.0293-0.0010.0413-0.00670.09945.567213.5847-24.3763
302.52630.8549-0.2682.8394-0.89612.44080.0296-0.1485-0.28060.1347-0.0817-0.08560.00580.13910.05210.06470.01490.0070.0588-0.03430.108310.416210.1311-18.0003
319.12992.00613.42653.2247-2.463610.95960.29490.3247-0.9607-0.3019-0.196-0.71970.81781.1649-0.0990.22390.11510.01940.2845-0.05120.328619.7228-23.549718.5238
323.5184-1.3622-0.12414.1431-0.44472.37980.15290.54580.1175-0.5879-0.1408-0.0348-0.09360.0004-0.0120.1204-0.0027-0.02120.23070.02310.06746.8602-6.393910.2136
332.9234-1.91091.09473.7229-1.33991.9604-0.02530.005-0.04190.07380.02650.3251-0.0553-0.2771-0.00110.1235-0.028-0.01690.1128-0.04710.1444-7.1216-14.412926.2614
343.2564-3.23081.7396.2152-3.5487.02870.08760.1575-0.42730.02520.07920.55890.2163-0.2463-0.16680.0837-0.0123-0.03420.0923-0.04730.1633-11.0298-16.541319.7788
351.8339-1.14870.61641.1138-0.78761.97050.07050.1416-0.1564-0.0155-0.0577-0.0131-0.01060.109-0.01280.08360.02420.02760.0849-0.01150.07084.1814-11.268322.4066
363.10330.95854.0841.41752.621711.0113-0.02590.266-0.0261-0.1832-0.01230.0705-0.10090.08790.03820.12390.0376-0.00390.04790.00810.1192-2.7996-9.788619.5907
376.082-2.745-1.58717.16381.68512.85840.0444-0.2716-0.1250.40280.03180.09910.19220.0074-0.07610.1253-0.0277-0.0020.08990.02860.06921.945-22.62337.1668
381.2749-0.1643-1.5856.3788-7.241910.76310.1077-0.12260.09720.83130.28020.3187-1.1478-0.2416-0.3880.1747-0.004-0.03390.2024-0.08080.2686-6.3605-3.84628.2618
392.404-0.7871.37991.2605-0.4865.54180.02620.136-0.0833-0.0344-0.08210.0617-0.2201-0.06780.05590.0483-0.0302-0.01170.0680.0240.08943.1012-9.603819.6406
402.6101-1.23981.14122.2991-1.44993.39240.08110.1313-0.1106-0.1754-0.0947-0.03370.19570.36620.01360.0575-0.0024-0.00470.0733-0.03570.078511.5701-15.11224.6814
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 15
2X-RAY DIFFRACTION2A16 - 41
3X-RAY DIFFRACTION3A42 - 69
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