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- PDB-2ctc: THE HIGH RESOLUTION CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN CARB... -

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Basic information

Entry
Database: PDB / ID: 2ctc
TitleTHE HIGH RESOLUTION CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN CARBOXYPEPTIDASE A AND L-PHENYL LACTATE
ComponentsCARBOXYPEPTIDASE A
KeywordsHYDROLASE(C-TERMINAL PEPTIDASE)
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
ALPHA-HYDROXY-BETA-PHENYL-PROPIONIC ACID / Carboxypeptidase A1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.4 Å
AuthorsTeplyakov, A. / Wilson, K.S. / Orioli, P. / Mangani, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1993
Title: High-resolution structure of the complex between carboxypeptidase A and L-phenyl lactate.
Authors: Teplyakov, A. / Wilson, K.S. / Orioli, P. / Mangani, S.
History
DepositionApr 2, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CARBOXYPEPTIDASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7493
Polymers34,5171
Non-polymers2322
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.600, 60.270, 47.250
Angle α, β, γ (deg.)90.00, 97.27, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: PEPTIDE BONDS BETWEEN RESIDUES SER 197 - TYR 198, PRO 205 - TYR 206, AND ARG 272 - ASP 273 ARE IN CIS CONFORMATION.

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Components

#1: Protein CARBOXYPEPTIDASE A


Mass: 34517.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P00730, carboxypeptidase A
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-HFA / ALPHA-HYDROXY-BETA-PHENYL-PROPIONIC ACID


Type: L-peptide linking / Mass: 166.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.11 Å3/Da / Density % sol: 41.73 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop / Details: referred to J.Mol.Biol. 19.423-441 1966
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.2 M1reservoirLiCl
20.02 MTris1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.45 Å / Lowest resolution: 3.5 Å / Num. obs: 46136 / % possible obs: 90.4 % / Num. measured all: 127939 / Rmerge(I) obs: 0.036

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementHighest resolution: 1.4 Å /
RfactorNum. reflection
obs0.16 4582
Refinement stepCycle: LAST / Highest resolution: 1.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2442 0 13 181 2636
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.45 Å / Num. reflection obs: 45829 / Rfactor obs: 0.161 / Lowest resolution: 8 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.014
X-RAY DIFFRACTIONp_angle_d0.037
X-RAY DIFFRACTIONp_planar_d0.054
X-RAY DIFFRACTIONp_plane_restr0.013
X-RAY DIFFRACTIONp_chiral_restr0.137

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