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- PDB-1dtd: CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE LEECH CARBOXYPEPTIDA... -

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Basic information

Entry
Database: PDB / ID: 1dtd
TitleCRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE LEECH CARBOXYPEPTIDASE INHIBITOR AND THE HUMAN CARBOXYPEPTIDASE A2 (LCI-CPA2)
Components
  • CARBOXYPEPTIDASE A2
  • METALLOCARBOXYPEPTIDASE INHIBITOR
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Carboxypeptidase A2 / Leech Carboxypeptidase Inhibitor / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


carboxypeptidase A2 / protein catabolic process in the vacuole / peptidase inhibitor activity / Developmental Lineage of Pancreatic Acinar Cells / vacuole / carboxypeptidase activity / metallocarboxypeptidase activity / proteolysis / extracellular space / extracellular region / zinc ion binding
Similarity search - Function
Carboxypeptidase inhibitor / Proteinase inhibitor I46, leech metallocarboxypeptidase inhibitor / Carboxypeptidase Inhibitor; Chain A / Carboxypeptidase A, carboxypeptidase domain / Carboxypeptidase, activation peptide / Metallocarboxypeptidase-like, propeptide / Carboxypeptidase activation peptide / Zinc carboxypeptidases, zinc-binding region 2 signature. / Zinc carboxypeptidases, zinc-binding region 1 signature. / Zn_pept ...Carboxypeptidase inhibitor / Proteinase inhibitor I46, leech metallocarboxypeptidase inhibitor / Carboxypeptidase Inhibitor; Chain A / Carboxypeptidase A, carboxypeptidase domain / Carboxypeptidase, activation peptide / Metallocarboxypeptidase-like, propeptide / Carboxypeptidase activation peptide / Zinc carboxypeptidases, zinc-binding region 2 signature. / Zinc carboxypeptidases, zinc-binding region 1 signature. / Zn_pept / Zinc carboxypeptidase / Peptidase family M14 domain profile. / Peptidase M14, carboxypeptidase A / Zn peptidases / Aminopeptidase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLUTAMIC ACID / Carboxypeptidase A2 / Metallocarboxypeptidase inhibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
Hirudo medicinalis (medicinal leech)
MethodX-RAY DIFFRACTION / Resolution: 1.65 Å
AuthorsReverter, D. / Fernandez-Catalan, C. / Bode, W. / Holak, T.A. / Aviles, F.X.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Structure of a novel leech carboxypeptidase inhibitor determined free in solution and in complex with human carboxypeptidase A2.
Authors: Reverter, D. / Fernandez-Catalan, C. / Baumgartner, R. / Pfander, R. / Huber, R. / Bode, W. / Vendrell, J. / Holak, T.A. / Aviles, F.X.
History
DepositionJan 12, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_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

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Assembly

Deposited unit
A: CARBOXYPEPTIDASE A2
B: METALLOCARBOXYPEPTIDASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6614
Polymers40,4492
Non-polymers2132
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-46 kcal/mol
Surface area14110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.439, 80.439, 114.464
Angle α, β, γ (deg.)90.0, 90.0, 120
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein CARBOXYPEPTIDASE A2


Mass: 33660.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P48052, peptidyl-dipeptidase A
#2: Protein METALLOCARBOXYPEPTIDASE INHIBITOR


Mass: 6787.647 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Hirudo medicinalis (medicinal leech) / References: UniProt: P81511
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.64 Å3/Da / Density % sol: 53.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: ammonium phosphate, sodium citrate, pH 7.5, VAPOR DIFFUSION, temperature 298.0K
Crystal grow
*PLUS
Temperature: 4, 20 ℃ / Method: vapor diffusion, sitting drop
Details: drop consists of equal volume of protein and reservoir solutions
PH range low: 8.5 / PH range high: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-15 mg/mlprotein1drop
20.1 M1dropNaCl
310 mMTris-HCl1drop
41.0 Mammonium phosphate1reservoir
50.1 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jan 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. all: 433570 / Num. obs: 52605 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 5 / Redundancy: 5 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 80
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 6 % / Rmerge(I) obs: 0.15 / Num. unique all: 3567 / % possible all: 98
Reflection
*PLUS
Num. measured all: 433570
Reflection shell
*PLUS
% possible obs: 98 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementResolution: 1.65→12 Å / σ(F): 2 / σ(I): 5
RfactorNum. reflection% reflection
Rfree0.234 5674 -
Rwork0.187 --
all0.187 48798 -
obs0.187 433567 98 %
Refinement stepCycle: LAST / Resolution: 1.65→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2843 0 11 231 3085
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d1.24
X-RAY DIFFRACTIONx_bond_d0.08
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.008
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.7

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