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- PDB-1lpb: THE 2.46 ANGSTROMS RESOLUTION STRUCTURE OF THE PANCREATIC LIPASE ... -

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Basic information

Entry
Database: PDB / ID: 1lpb
TitleTHE 2.46 ANGSTROMS RESOLUTION STRUCTURE OF THE PANCREATIC LIPASE COLIPASE COMPLEX INHIBITED BY A C11 ALKYL PHOSPHONATE
Components
  • COLIPASE
  • LIPASE
KeywordsHYDROLASE(CARBOXYLIC ESTERASE)
Function / homology
Function and homology information


positive regulation of triglyceride lipase activity / Digestion of dietary lipid / Retinoid metabolism and transport / all-trans-retinyl-palmitate hydrolase, all-trans-retinol forming activity / Digestion of dietary lipid / lipoprotein lipase activity / lipase binding / phospholipase A1 activity / triglyceride catabolic process / lipase activity ...positive regulation of triglyceride lipase activity / Digestion of dietary lipid / Retinoid metabolism and transport / all-trans-retinyl-palmitate hydrolase, all-trans-retinol forming activity / Digestion of dietary lipid / lipoprotein lipase activity / lipase binding / phospholipase A1 activity / triglyceride catabolic process / lipase activity / intestinal cholesterol absorption / high-density lipoprotein particle remodeling / triacylglycerol lipase / triacylglycerol lipase activity / Developmental Lineage of Pancreatic Acinar Cells / response to food / retinoid metabolic process / Retinoid metabolism and transport / lipid catabolic process / digestion / cholesterol homeostasis / response to bacterium / enzyme activator activity / lipid metabolic process / fatty acid biosynthetic process / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Colipase / Colipase, N-terminal / Colipase, C-terminal / Colipase, conserved site / : / Colipase, N-terminal domain / Colipase, C-terminal domain / Colipase signature. / Colipase family profile. / Colipase ...Colipase / Colipase, N-terminal / Colipase, C-terminal / Colipase, conserved site / : / Colipase, N-terminal domain / Colipase, C-terminal domain / Colipase signature. / Colipase family profile. / Colipase / Pancreatic lipase / Lipase, subunit A / Lipase, subunit A / Lipase, LIPH-type / Lipase, N-terminal / Triacylglycerol lipase family / Lipase / Lipase / PLAT/LH2 domain / Lipoxygenase-1 / Lipoxygenase homology 2 (beta barrel) domain / PLAT/LH2 domain / PLAT/LH2 domain superfamily / PLAT/LH2 domain / PLAT domain profile. / Lipases, serine active site. / Ribbon / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
METHOXYUNDECYLPHOSPHINIC ACID / Colipase / Pancreatic triacylglycerol lipase
Similarity search - Component
Biological speciesSus scrofa (pig)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.46 Å
AuthorsEgloff, M.-P. / Van Tilbeurgh, H. / Cambillau, C.
Citation
Journal: Biochemistry / Year: 1995
Title: The 2.46 A resolution structure of the pancreatic lipase-colipase complex inhibited by a C11 alkyl phosphonate.
Authors: Egloff, M.P. / Marguet, F. / Buono, G. / Verger, R. / Cambillau, C. / van Tilbeurgh, H.
#1: Journal: Nature / Year: 1993
Title: Interfacial Activation of the Lipase-Procolipase Complex by Mixed Micelles Revealed by X-Ray Crystallography
Authors: Van Tilbeurgh, H. / Egloff, M.-P. / Martinez, C. / Rugani, N. / Verger, R. / Cambillau, C.
#2: Journal: Nature / Year: 1992
Title: Structure of the Pancreatic Lipase-Procolipase Complex
Authors: Van Tilbeurgh, H. / Sarda, L. / Verger, R. / Cambillau, C.
History
DepositionAug 19, 1994Processing site: BNL
Revision 1.0Nov 1, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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
Revision 1.4Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COLIPASE
B: LIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6459
Polymers59,8932
Non-polymers1,7527
Water5,134285
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.700, 133.700, 93.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Atom site foot note1: CIS PROLINE - PRO B 16 / 2: CIS PROLINE - PRO B 211 / 3: CIS PROLINE - PRO B 298

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein COLIPASE


Mass: 10319.651 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P02703
#2: Protein LIPASE


Mass: 49573.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: PANCREAS / References: UniProt: P16233, triacylglycerol lipase

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Sugars , 1 types, 5 molecules

#3: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 3 types, 287 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-MUP / METHOXYUNDECYLPHOSPHINIC ACID


Mass: 250.315 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H27O3P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsUSE OF PARTIAL OCCUPANCY FOR THE INHIBITOR (REFINED OCCUPANCY) AND FOR BETA-OCTYLGLUCOSIDE MOLECULES.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.48 Å3/Da / Density % sol: 64.65 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mllipase1drop
22.5 mg/mlcolipase1drop
32 %PEG80001drop
40.1 MMES1drop
50.4 M1dropNaCl
6250 mMbeta-glucoside1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.46 Å / Lowest resolution: 20 Å / Num. obs: 29845 / % possible obs: 92 % / Redundancy: 9.4 % / Num. measured all: 271893 / Rmerge(I) obs: 0.106
Reflection shell
*PLUS
Highest resolution: 2.46 Å / Lowest resolution: 2.53 Å / % possible obs: 77.8 % / Redundancy: 3.9 % / Mean I/σ(I) obs: 84.9

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.46→6 Å / Rfactor Rfree: 0.285 / Rfactor Rwork: 0.183 / Rfactor obs: 0.183 / σ(F): 1
Refinement stepCycle: LAST / Resolution: 2.46→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5060 0 199 855 6114
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.96
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 27738 / Rfactor obs: 0.183 / Rfactor Rfree: 0.285
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.96

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