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- PDB-1bav: CARBOXYPEPTIDASE A COMPLEXED WITH 2-BENZYL-3-IODO-PROPANOIC ACID (BIP) -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1bav
TitleCARBOXYPEPTIDASE A COMPLEXED WITH 2-BENZYL-3-IODO-PROPANOIC ACID (BIP)
ComponentsCARBOXYPEPTIDASE A
KeywordsCARBOXYPEPTIDASE / HYDROLASE / ZINC / ZYMOGEN
Function / homology
Function and homology information


carboxypeptidase A / leukotriene metabolic process / metallocarboxypeptidase activity / proteolysis / extracellular space / zinc ion binding
Similarity search - Function
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. / Peptidase family M14 domain profile. / Zn_pept / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase ...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. / Peptidase family M14 domain profile. / Zn_pept / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-BENZYL-3-IODOPROPANOIC ACID / Carboxypeptidase A1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsMartin, P. / Edwards, B.
CitationJournal: J.Am.Chem.Soc. / Year: 1996
Title: Crystallographic and computational insight on the mechanism of zinc-ion-dependent inactivation of carboxypeptidase a by 2-benzyl-3-iodopropanoate.
Authors: Massova, I. / Martin, P. / deMel, S. / Tanaka, Y. / Edwards, B. / Mobashery, S.
History
DepositionNov 14, 1996-
Revision 1.0Apr 1, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CARBOXYPEPTIDASE A
B: CARBOXYPEPTIDASE A
C: CARBOXYPEPTIDASE A
D: CARBOXYPEPTIDASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,29712
Polymers138,8754
Non-polymers1,4228
Water10,359575
1
A: CARBOXYPEPTIDASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0743
Polymers34,7191
Non-polymers3562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CARBOXYPEPTIDASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0743
Polymers34,7191
Non-polymers3562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: CARBOXYPEPTIDASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0743
Polymers34,7191
Non-polymers3562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: CARBOXYPEPTIDASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0743
Polymers34,7191
Non-polymers3562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.700, 60.500, 91.800
Angle α, β, γ (deg.)90.00, 97.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
CARBOXYPEPTIDASE A /


Mass: 34718.793 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P00730, carboxypeptidase A
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-BIP / 2-BENZYL-3-IODOPROPANOIC ACID


Mass: 290.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H11IO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 575 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.32 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.2 M1reservoirLiCl
20.02 MTris-HCl1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.6 Å / Num. obs: 65817 / Rmerge(I) obs: 0.039

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementRfactor Rfree: 0.213 / Rfactor Rwork: 0.172 / Rfactor obs: 0.172 / Highest resolution: 1.6 Å
Refinement stepCycle: LAST / Highest resolution: 1.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9744 0 52 575 10371
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.6
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Lowest resolution: 7 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.6

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