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- PDB-1huc: THE REFINED 2.15 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF HUMAN LIVER... -

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Entry
Database: PDB / ID: 1huc
TitleTHE REFINED 2.15 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF HUMAN LIVER CATHEPSIN B: THE STRUCTURAL BASIS FOR ITS SPECIFICITY
Components(CATHEPSIN B) x 2
KeywordsTHIOL PROTEASE
Function / homology
Function and homology information


cathepsin B / peptidase inhibitor complex / endolysosome lumen / thyroid hormone generation / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / decidualization / Collagen degradation ...cathepsin B / peptidase inhibitor complex / endolysosome lumen / thyroid hormone generation / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / decidualization / Collagen degradation / collagen catabolic process / collagen binding / epithelial cell differentiation / MHC class II antigen presentation / cysteine-type peptidase activity / proteolysis involved in protein catabolic process / melanosome / peptidase activity / : / regulation of apoptotic process / ficolin-1-rich granule lumen / lysosome / apical plasma membrane / external side of plasma membrane / cysteine-type endopeptidase activity / Neutrophil degranulation / symbiont entry into host cell / perinuclear region of cytoplasm / proteolysis / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Peptidase C1A, propeptide / Peptidase family C1 propeptide / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal / Papain family cysteine protease ...Peptidase C1A, propeptide / Peptidase family C1 propeptide / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsMusil, D. / Bode, W.
CitationJournal: EMBO J. / Year: 1991
Title: The refined 2.15 A X-ray crystal structure of human liver cathepsin B: the structural basis for its specificity.
Authors: Musil, D. / Zucic, D. / Turk, D. / Engh, R.A. / Mayr, I. / Huber, R. / Popovic, T. / Turk, V. / Towatari, T. / Katunuma, N. / Bode, W.
History
DepositionApr 21, 1993Processing site: BNL
Revision 1.0Jan 26, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CATHEPSIN B
B: CATHEPSIN B
C: CATHEPSIN B
D: CATHEPSIN B


Theoretical massNumber of molelcules
Total (without water)55,3044
Polymers55,3044
Non-polymers00
Water5,098283
1
A: CATHEPSIN B
B: CATHEPSIN B


Theoretical massNumber of molelcules
Total (without water)27,6522
Polymers27,6522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-30 kcal/mol
Surface area11230 Å2
MethodPISA
2
C: CATHEPSIN B
D: CATHEPSIN B


Theoretical massNumber of molelcules
Total (without water)27,6522
Polymers27,6522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-29 kcal/mol
Surface area11280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.230, 34.160, 85.560
Angle α, β, γ (deg.)90.00, 102.90, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: ASN B 113 - GLY B 114 OMEGA = 210.44 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: CIS PROLINE - PRO B 138 / 3: CIS PROLINE - PRO D 138
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.019, -0.0043, -0.9998), (0.0196, 0.9998, -0.0047), (0.9996, -0.0197, -0.0189)
Vector: 83.76, -24.898, 20.754)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAINS *A* AND *B* WHEN APPLIED TO CHAINS *C* AND *D*, RESPECTIVELY.

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Components

#1: Protein/peptide CATHEPSIN B


Mass: 5213.840 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P07858, cathepsin B
#2: Protein CATHEPSIN B


Mass: 22437.910 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P07858, cathepsin B
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.59 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.4-1.5 Msodium phosphate1reservoir
21.1-1.25 Mammonium sulphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
X-PLORmodel building
EREFrefinement
X-PLORrefinement
X-PLORphasing
RefinementRfactor obs: 0.164 / Highest resolution: 2.1 Å
Refinement stepCycle: LAST / Highest resolution: 2.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3876 0 0 283 4159
Refinement
*PLUS
Highest resolution: 2.15 Å / Lowest resolution: 8 Å / Rfactor obs: 0.164
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.015
X-RAY DIFFRACTIONo_angle_deg2.565

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