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- PDB-5lyf: Crystal structure of 1 in complex with tafCPB -

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Basic information

Entry
Database: PDB / ID: 5lyf
TitleCrystal structure of 1 in complex with tafCPB
ComponentsCarboxypeptidase B
KeywordsHYDROLASE / tafinized carboxypeptidase B / HYRDROLASE
Function / homology
Function and homology information


carboxypeptidase B / metallocarboxypeptidase activity / cytoplasmic vesicle / proteolysis / extracellular space / zinc ion binding
Similarity search - Function
Carboxypeptidase B, 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 B, 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
Chem-7B6 / Carboxypeptidase B
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.01 Å
AuthorsSchreuder, H. / Liesum, A. / Loenze, P.
CitationJournal: J. Med. Chem. / Year: 2016
Title: Sulfamide as Zinc Binding Motif in Small Molecule Inhibitors of Activated Thrombin Activatable Fibrinolysis Inhibitor (TAFIa).
Authors: Halland, N. / Czech, J. / Czechtizky, W. / Evers, A. / Follmann, M. / Kohlmann, M. / Schreuder, H.A. / Kallus, C.
History
DepositionSep 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carboxypeptidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4935
Polymers34,8601
Non-polymers6334
Water10,485582
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-36 kcal/mol
Surface area11900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.490, 81.490, 95.734
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-923-

HOH

21A-950-

HOH

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Components

#1: Protein Carboxypeptidase B /


Mass: 34859.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: CPB1, CPB / Production host: Komagataella pastoris CBS 7435 (fungus) / References: UniProt: P09955, carboxypeptidase B
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-7B6 / (2~{S})-6-azanyl-2-[[(2~{R})-1-[[(1~{R},2~{S},4~{S})-2-bicyclo[2.2.1]heptanyl]amino]-3-cyclohexyl-1-oxidanylidene-propan-2-yl]carbamoylamino]hexanoic acid


Mass: 436.588 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H40N4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 582 / 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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: THE PURIFIED PROTEIN WAS DISSOLVED IN 50 MM TRIS-HCL, PH 7.5 AND CONCENTRATED TO 11 MG/ML. 1 UL OF PROTEIN SOLUTION WAS EQUILIBRATED AGAINST 1 UL OF RESERVOIR SOLUTIONS CONTAINING 16-20% ...Details: THE PURIFIED PROTEIN WAS DISSOLVED IN 50 MM TRIS-HCL, PH 7.5 AND CONCENTRATED TO 11 MG/ML. 1 UL OF PROTEIN SOLUTION WAS EQUILIBRATED AGAINST 1 UL OF RESERVOIR SOLUTIONS CONTAINING 16-20% PEG3350, 100 MM MES PH 5.5 AND 50 MM ZNACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 29, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.01→81.42 Å / Num. obs: 21825 / % possible obs: 98.7 % / Observed criterion σ(F): -3 / Redundancy: 10.4 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 15.7
Reflection shellResolution: 2.01→2.1 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 7.99 / % possible all: 90.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
REFMAC5.2.0019phasing
RefinementResolution: 2.01→49.39 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.845 / SU B: 6.973 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.245 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30479 1522 7 %RANDOM
Rwork0.18355 ---
obs0.19202 20300 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 21.074 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2---0.13 Å20 Å2
3---0.25 Å2
Refinement stepCycle: 1 / Resolution: 2.01→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2446 0 34 582 3062
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222552
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9561.9453476
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2525304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3524.034119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.96515395
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6511510
X-RAY DIFFRACTIONr_chiral_restr0.1510.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021964
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2520.21471
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.21719
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2670.2420
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0570.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3110.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2780.243
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2720.22
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0961.51560
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.66322439
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.59131191
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5124.51037
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: 2.013→2.065 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 83 -
Rwork0.238 1354 -
obs--90.21 %

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