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- PDB-3nxq: Angiotensin Converting Enzyme N domain glycsoylation mutant (Ndom... -

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Basic information

Entry
Database: PDB / ID: 3nxq
TitleAngiotensin Converting Enzyme N domain glycsoylation mutant (Ndom389) in complex with RXP407
ComponentsAngiotensin-converting enzyme
KeywordsHYDROLASE/HYDROLASE INHIBITOR / dicarboxy zinc metallopeptidase / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


mononuclear cell proliferation / cell proliferation in bone marrow / bradykinin receptor binding / regulation of angiotensin metabolic process / exopeptidase activity / substance P catabolic process / peptidyl-dipeptidase A / tripeptidyl-peptidase activity / regulation of renal output by angiotensin / negative regulation of calcium ion import ...mononuclear cell proliferation / cell proliferation in bone marrow / bradykinin receptor binding / regulation of angiotensin metabolic process / exopeptidase activity / substance P catabolic process / peptidyl-dipeptidase A / tripeptidyl-peptidase activity / regulation of renal output by angiotensin / negative regulation of calcium ion import / positive regulation of peptidyl-cysteine S-nitrosylation / response to laminar fluid shear stress / negative regulation of gap junction assembly / metallodipeptidase activity / positive regulation of systemic arterial blood pressure / cellular response to aldosterone / hormone catabolic process / bradykinin catabolic process / angiogenesis involved in coronary vascular morphogenesis / response to thyroid hormone / antigen processing and presentation of peptide antigen via MHC class I / negative regulation of glucose import / vasoconstriction / hormone metabolic process / neutrophil mediated immunity / regulation of smooth muscle cell migration / regulation of hematopoietic stem cell proliferation / mitogen-activated protein kinase binding / embryo development ending in birth or egg hatching / chloride ion binding / mitogen-activated protein kinase kinase binding / positive regulation of neurogenesis / arachidonic acid secretion / post-transcriptional regulation of gene expression / eating behavior / heterocyclic compound binding / lung alveolus development / heart contraction / peptide catabolic process / response to dexamethasone / regulation of heart rate by cardiac conduction / regulation of systemic arterial blood pressure by renin-angiotensin / regulation of vasoconstriction / peptidyl-dipeptidase activity / hematopoietic stem cell differentiation / blood vessel remodeling / angiotensin maturation / amyloid-beta metabolic process / animal organ regeneration / Metabolism of Angiotensinogen to Angiotensins / carboxypeptidase activity / positive regulation of vasoconstriction / sperm midpiece / blood vessel diameter maintenance / response to nutrient levels / basal plasma membrane / kidney development / angiotensin-activated signaling pathway / female pregnancy / cellular response to glucose stimulus / brush border membrane / regulation of synaptic plasticity / metalloendopeptidase activity / regulation of blood pressure / metallopeptidase activity / male gonad development / actin binding / peptidase activity / spermatogenesis / endopeptidase activity / response to lipopolysaccharide / lysosome / calmodulin binding / response to hypoxia / endosome / response to xenobiotic stimulus / positive regulation of apoptotic process / external side of plasma membrane / negative regulation of gene expression / proteolysis / extracellular space / zinc ion binding / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Peptidase family M2 domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
RXP407 / DI(HYDROXYETHYL)ETHER / Chem-RX4 / Angiotensin-converting enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsAnthony, C.S. / Corradi, H.R. / Schwager, S.L.U. / Redelinghuys, P. / Georgiadis, D. / Dive, V. / Acharya, K.R. / Sturrock, E.D.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: The N domain of human angiotensin-I-converting enzyme: the role of N-glycosylation and the crystal structure in complex with an N domain-specific phosphinic inhibitor, RXP407.
Authors: Anthony, C.S. / Corradi, H.R. / Schwager, S.L. / Redelinghuys, P. / Georgiadis, D. / Dive, V. / Acharya, K.R. / Sturrock, E.D.
History
DepositionJul 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 12, 2012Group: Other
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref_seq_dif / 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.type_symbol / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_molecule.asym_id / _pdbx_struct_assembly_gen.asym_id_list / _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_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 / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Angiotensin-converting enzyme
B: Angiotensin-converting enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,62620
Polymers145,2132
Non-polymers5,41318
Water10,142563
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A: Angiotensin-converting enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1199
Polymers72,6071
Non-polymers2,5128
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Angiotensin-converting enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,50711
Polymers72,6071
Non-polymers2,90110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.882, 76.685, 82.646
Angle α, β, γ (deg.)88.63, 64.17, 75.70
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Angiotensin-converting enzyme / ACE / Dipeptidyl carboxypeptidase I / Kininase II / Angiotensin-converting enzyme / soluble form


Mass: 72606.508 Da / Num. of mol.: 2 / Fragment: N domain (UNP residues 30-657)
Mutation: N9Q, N25Q, N82Q, N117Q, N131Q, N289Q, Q545R, P576L, R629L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACE, DCP, DCP1 / Cell line (production host): ovary cells / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: P12821, peptidyl-dipeptidase A, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds

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Sugars , 3 types, 6 molecules

#2: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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Non-polymers , 7 types, 575 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-RX4 / N~2~-acetyl-N-{(1R)-1-[(S)-[(2S)-3-{[(2S)-1-amino-1-oxopropan-2-yl]amino}-2-methyl-3-oxopropyl](hydroxy)phosphoryl]-2-phenylethyl}-L-alpha-asparagine / Ac-Asp-(L)Phe(PO2CH2)(L)Ala-Ala-NH2 / RXP407


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 498.467 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H31N4O8P / References: RXP407
#7: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#10: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 563 / 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: 2.76 Å3/Da / Density % sol: 55.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 150nl condition Morpheus A9 (0.06M divalents, 0.1M Tris/Bicine pH 8.5, 30% PEG550mme/PEG20K) and 150nl additive G10 (0.2% w/v 1,4-Cyclohexanedicarboxylic acid, 0.2% w/v 2,5- ...Details: 150nl condition Morpheus A9 (0.06M divalents, 0.1M Tris/Bicine pH 8.5, 30% PEG550mme/PEG20K) and 150nl additive G10 (0.2% w/v 1,4-Cyclohexanedicarboxylic acid, 0.2% w/v 2,5-Pyridinedicarboxylic acid, 0.2% w/v Glutaric acid, 0.2% w/v trans-1,2-Cyclohexanedicarboxylic acid, 0.2% w/v trans-Aconitic acid, 0.02 M HEPES sodium pH 6.8) , VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 106279 / Rsym value: 0.054 / Net I/σ(I): 12.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→40.81 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.486 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23719 1025 1 %RANDOM
Rwork0.19398 ---
obs0.19441 100680 95.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.813 Å2
Baniso -1Baniso -2Baniso -3
1--1.65 Å21.2 Å21.24 Å2
2---0.28 Å20.14 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.99→40.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9844 0 343 563 10750
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02110567
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0641.96714420
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8851232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.23223.673520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.91151571
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3091565
X-RAY DIFFRACTIONr_chiral_restr0.0790.21525
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218221
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_it0.3961.56128
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.78429854
X-RAY DIFFRACTIONr_scbond_it1.2534439
X-RAY DIFFRACTIONr_scangle_it2.1664.54557
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.991→2.043 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 78 -
Rwork0.261 7149 -
obs--92.02 %
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)
10.94220.5369-1.21921.0142-1.04231.89950.09290.0587-0.1418-0.001-0.08550.0996-0.0768-0.0523-0.00740.06390.0108-0.08490.1159-0.01430.1778-23.8762-22.7001-18.2247
21.0476-0.11290.09720.57140.09080.14450.048-0.00340.0441-0.0754-0.0018-0.04-0.0471-0.0098-0.04620.13570.01240.00360.10230.00210.07513.9193-5.4908-17.6816
31.1513-0.222-0.24260.65130.08310.52640.05330.0342-0.037-0.0928-0.0645-0.0202-0.058-0.05250.01120.11050.0069-0.01080.1321-0.00980.08573.7101-25.4366-28.4258
40.251-0.1094-0.00980.58020.11240.15070.0096-0.0714-0.02570.016-0.0042-0.0267-0.0289-0.0237-0.00540.11990.0025-0.00830.1368-0.00220.10195.2331-16.2348-12.908
51.00610.2374-0.22431.06110.15730.52380.0357-0.0856-0.00330.04850.0557-0.2152-0.0373-0.0036-0.09140.0881-0.0091-0.01510.1283-0.02870.067918.1312-8.521-9.0726
62.58582.188-1.31493.3757-1.38750.7797-0.18230.0333-0.03830.0870.1625-0.02430.1283-0.00420.01980.17620.019-0.00720.12130.01790.050.6933-3.949237.2204
70.2381-0.311-0.00450.75190.02810.96760.0368-0.0017-0.0191-0.086-0.0179-0.042-0.04450.0575-0.01890.1082-0.0126-0.00420.0835-0.01710.09454.557314.524110.5627
80.7843-0.4748-0.10721.1720.15740.6885-0.0125-0.077-0.02620.02620.0061-0.0488-0.069-0.06220.00640.1167-0.0080.00930.1199-0.00330.088-4.653822.692229.5599
90.3791-0.2775-0.22850.32820.39440.81340.04960.0076-0.0818-0.0843-0.05640.0495-0.0021-0.12450.00680.1127-0.0087-0.01580.12-0.01420.116-7.711115.444114.0803
100.81570.1257-0.46521.0139-0.12971.77050.04170.0745-0.0872-0.2137-0.10230.1019-0.2122-0.21040.06050.13110.0152-0.04270.0702-0.02290.0364-8.062220.36790.129
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 98
2X-RAY DIFFRACTION2A99 - 278
3X-RAY DIFFRACTION3A279 - 416
4X-RAY DIFFRACTION4A417 - 558
5X-RAY DIFFRACTION5A559 - 610
6X-RAY DIFFRACTION6B1 - 96
7X-RAY DIFFRACTION7B97 - 275
8X-RAY DIFFRACTION8B276 - 406
9X-RAY DIFFRACTION9B407 - 558
10X-RAY DIFFRACTION10B559 - 610

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