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- PDB-1bbs: X-RAY ANALYSES OF PEPTIDE INHIBITOR COMPLEXES DEFINE THE STRUCTUR... -

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Basic information

Entry
Database: PDB / ID: 1bbs
TitleX-RAY ANALYSES OF PEPTIDE INHIBITOR COMPLEXES DEFINE THE STRUCTURAL BASIS OF SPECIFICITY FOR HUMAN AND MOUSE RENINS
ComponentsRENIN
KeywordsASPARTIC PROTEINASE
Function / homology
Function and homology information


renin / mesonephros development / juxtaglomerular apparatus development / response to cGMP / renin-angiotensin regulation of aldosterone production / drinking behavior / response to immobilization stress / regulation of MAPK cascade / response to cAMP / amyloid-beta metabolic process ...renin / mesonephros development / juxtaglomerular apparatus development / response to cGMP / renin-angiotensin regulation of aldosterone production / drinking behavior / response to immobilization stress / regulation of MAPK cascade / response to cAMP / amyloid-beta metabolic process / Metabolism of Angiotensinogen to Angiotensins / cell maturation / angiotensin maturation / hormone-mediated signaling pathway / insulin-like growth factor receptor binding / kidney development / regulation of blood pressure / male gonad development / cellular response to xenobiotic stimulus / apical part of cell / peptidase activity / response to lipopolysaccharide / aspartic-type endopeptidase activity / signaling receptor binding / proteolysis / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Renin-like domain / Aspartic peptidase, N-terminal / A1 Propeptide / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site ...Renin-like domain / Aspartic peptidase, N-terminal / A1 Propeptide / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsDhanaraj, V. / Blundell, T.L.
CitationJournal: Nature / Year: 1992
Title: X-ray analyses of peptide-inhibitor complexes define the structural basis of specificity for human and mouse renins.
Authors: Dhanaraj, V. / Dealwis, C.G. / Frazao, C. / Badasso, M. / Sibanda, B.L. / Tickle, I.J. / Cooper, J.B. / Driessen, H.P. / Newman, M. / Aguilar, C. / Wood, S.P. / Blundell, T.L. / Hobart, P.M. ...Authors: Dhanaraj, V. / Dealwis, C.G. / Frazao, C. / Badasso, M. / Sibanda, B.L. / Tickle, I.J. / Cooper, J.B. / Driessen, H.P. / Newman, M. / Aguilar, C. / Wood, S.P. / Blundell, T.L. / Hobart, P.M. / Geoghegan, K.F. / Ammirati, M.J. / Danley, D.E.
History
DepositionMay 21, 1992Processing site: BNL
Revision 1.0Jan 31, 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 1.4Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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: RENIN
B: RENIN


Theoretical massNumber of molelcules
Total (without water)74,5342
Polymers74,5342
Non-polymers00
Water00
1
A: RENIN


Theoretical massNumber of molelcules
Total (without water)37,2671
Polymers37,2671
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RENIN


Theoretical massNumber of molelcules
Total (without water)37,2671
Polymers37,2671
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: RENIN
B: RENIN

A: RENIN
B: RENIN

A: RENIN
B: RENIN


Theoretical massNumber of molelcules
Total (without water)223,6026
Polymers223,6026
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area10650 Å2
ΔGint-57 kcal/mol
Surface area75440 Å2
MethodPISA
4
A: RENIN

A: RENIN

A: RENIN


Theoretical massNumber of molelcules
Total (without water)111,8013
Polymers111,8013
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area3240 Å2
ΔGint-25 kcal/mol
Surface area39840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.100, 143.100, 143.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Atom site foot note1: CIS PROLINE - PRO 23 / 2: CIS PROLINE - PRO 111 / 3: CIS PROLINE - PRO 294 / 4: CIS PROLINE - PRO 297
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.7821, -0.3605, -0.5084), (-0.3398, -0.4371, 0.8327), (-0.5224, 0.824, 0.2193)
Vector: 118.31, 34.34, 15.98)
DetailsTHIS ENTRY CONTAINS ONLY ONE OF THE TWO PROTEIN CHAINS IN CRYSTALLOGRAPHIC ASYMMETRIC UNIT. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW MAY BE USED TO GENERATE THE RELATED PROTEIN CHAIN.

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Components

#1: Protein RENIN


Mass: 37267.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P00797, renin
Has protein modificationY
Sequence detailsTHE REVISED 'PEPSIN NUMBERING' SCHEME IS USED FOR NUMBERING THE RESIDUES.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.28 Å3/Da / Density % sol: 62.44 %
Crystal
*PLUS
Density % sol: 59.8 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
220 mMTris-HCl1drop
30.6 M1reservoirprecipitantNaCl
450 mMsodium citrate1reservoirprecipitant
510 %(w/v)PEG40001reservoirprecipitant

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 22383 / % possible obs: 88.6 % / Rmerge(I) obs: 0.076

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Processing

SoftwareName: RESTRAIN / Classification: refinement
RefinementRfactor obs: 0.196 / Highest resolution: 2.8 Å
Refinement stepCycle: LAST / Highest resolution: 2.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5018 0 0 0 5018
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d0.025
Software
*PLUS
Name: RESTRAIN / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / Num. reflection obs: 21297 / Rfactor obs: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS

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