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- PDB-4uib: Crystal structure of 3p in complex with tafCPB -

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Basic information

Entry
Database: PDB / ID: 4uib
TitleCrystal structure of 3p in complex with tafCPB
ComponentsCARBOXYPEPTIDASE B
KeywordsHYDROLASE / TAFI / THROMBOSIS / FIBRINOLYSIS / DRUG DISCOVERY
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
ACETATE ION / Chem-GWX / Carboxypeptidase B
Similarity search - Component
Biological speciesSUS SCROFA (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsHalland, N. / Broenstrup, M. / Czech, J. / Czechtizky, W. / Evers, A. / Follmann, M. / Kohlmann, M. / Schiell, M. / Kurz, M. / Schreuder, H.A. / Kallus, C.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Novel Small Molecule Inhibitors of Activated Thrombin Activatable Fibrinolysis Inhibitor (Tafia) from Natural Product Anabaenopeptin.
Authors: Halland, N. / Bronstrup, M. / Czech, J. / Czechtizky, W. / Evers, A. / Follmann, M. / Kohlmann, M. / Schiell, M. / Kurz, M. / Schreuder, H.A. / Kallus, C.
History
DepositionMar 27, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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

Downloads & links

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Assembly

Deposited unit
A: CARBOXYPEPTIDASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,96210
Polymers34,8601
Non-polymers1,1029
Water8,341463
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.530, 82.530, 95.397
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-1312-

ZN

21A-2136-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CARBOXYPEPTIDASE B / TAFCPB


Mass: 34859.969 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 111-416 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: CONTAINS CATALYTIC ZINC ION. / Source: (gene. exp.) SUS SCROFA (pig) / Production host: PICHIA PASTORIS (fungus) / Strain (production host): GS115 / References: UniProt: P09955, carboxypeptidase B

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Non-polymers , 5 types, 472 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-GWX / (2S)-6-AMINO-2-[[(1R)-1-(CYCLOHEXYLMETHYL)-2-OXO-2-[[(2S)-1,7,7-TRIMETHYLNORBORNAN-2-YL]AMINO]ETHYL]ARBAMOYLAMINO]HEXANOIC ACID


Mass: 478.668 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H46N4O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence details8 RESIDUES ARE MUTATED. F175I, T302S, M309H, L311V, I355L, P357L, A359P AND S362G.

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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: 2.35 Å3/Da / Density % sol: 47.6 % / Description: NONE
Crystal growpH: 7.5
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: ID29 / Wavelength: 0.976251
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2013 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 1.94→95.4 Å / Num. obs: 24986 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 13.59 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 22.6
Reflection shellResolution: 1.94→2.05 Å / Redundancy: 13 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 7.1 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PREVIOUSLY SOLVED IN-HOUSE STRUCTURE

Resolution: 1.94→62.41 Å / Cor.coef. Fo:Fc: 0.9442 / Cor.coef. Fo:Fc free: 0.9303 / SU R Cruickshank DPI: 0.154 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.183 / SU Rfree Blow DPI: 0.138 / SU Rfree Cruickshank DPI: 0.129
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=3004. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=3004. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=3.
RfactorNum. reflection% reflectionSelection details
Rfree0.1917 1269 5.09 %RANDOM
Rwork0.165 ---
obs0.1664 24928 99.58 %-
Displacement parametersBiso mean: 14.83 Å2
Baniso -1Baniso -2Baniso -3
1--1.0019 Å20 Å20 Å2
2---1.0019 Å20 Å2
3---2.0038 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 1.94→62.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2446 0 65 463 2974
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0072614HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.913560HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d880SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes60HARMONIC2
X-RAY DIFFRACTIONt_gen_planes377HARMONIC5
X-RAY DIFFRACTIONt_it2614HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.7
X-RAY DIFFRACTIONt_other_torsion14.82
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion338SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies5HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3529SEMIHARMONIC4
LS refinement shellResolution: 1.94→2.02 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2844 140 5.25 %
Rwork0.2444 2527 -
all0.2465 2667 -
obs--99.58 %

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