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Title :   STRUCTURE OF A PEPSIN(SLASH)RENIN INHIBITOR COMPLEX REVEALS A NOVEL CRYSTAL PACKING INDUCED BY MINOR CHEMICAL ALTERATIONS IN THE INHIBITOR

Authors :   L. Chen, C. Abad-Zapatero

Date :   22 Oct 91 (Deposition) - 31 Jan 94 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym./Biol. Unit : A,B

Keywords :   Acid Proteinase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Chen, J. W. Erickson, T. J. Rydel, C. H. Park, D. Neidhart, J. Luly, C. Abad-Zapatero
Structure Of A Pepsin/Renin Inhibitor Complex Reveals A Novel Crystal Packing Induced By Minor Chemical Alterations In The Inhibitor.
Acta Crystallogr. , Sect. B V. 48 476 1992
PubMed-ID: 1418819 | Reference-DOI: 10.1107/S0108768192001939
(for further references see the PDB file header)

Molecule 1 - PEPSIN A
	Chains	:	A, B
	EC Number	:	3.4.23.1
	Engineered	:	YES
	Organism Common	:	PIG
	Organism Scientific	:	SUS SCROFA
	Organism Taxid	:	9823

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	0ZL	2	Ligand/Ion	N-(ETHOXYCARBONYL)-L-LEUCYL-N-[(1R,2S,3S)-1-(CYCLOHEXYLMETHYL)-2,3-DIHYDROXY-5-METHYLHEXYL]-L-LEUCINAMIDE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:32 , GLY A:34 , TYR A:75 , GLY A:76 , THR A:77 , ILE A:120 , ILE A:213 , ASP A:215 , GLY A:217 , THR A:218 , SER A:219 , MET A:289 , ILE A:300 , HOH A:347	BINDING SITE FOR RESIDUE 0ZL A 327
2	AC2	SOFTWARE	ILE B:30 , ASP B:32 , GLY B:34 , TYR B:75 , GLY B:76 , THR B:77 , PHE B:111 , PHE B:117 , TYR B:189 , ILE B:213 , ASP B:215 , GLY B:217 , THR B:218 , SER B:219 , MET B:289 , HOH B:339	BINDING SITE FOR RESIDUE 0ZL B 327

Asymmetric/Biological Unit

No.	Residues
1	A:45	-	A:50
2	A:206	-	A:210
3	A:249	-	A:282
4	B:45	-	B:50
5	B:206	-	B:210
6	B:249	-	B:282

Asymmetric/Biological Unit

No.	Residues
1	Thr A:22	-	Pro A:23
2	Thr B:22	-	Pro B:23

(no "SAP(SNP)/Variant" information available for 1PSA)

Asymmetric/Biological Unit (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEPTIDASE_A1	PS51767	Peptidase family A1 domain profile.	PEPA_PIG	73-382	2	A:14-323 B:14-323
2	ASP_PROTEASE	PS00141	Eukaryotic and viral aspartyl proteases active site.	PEPA_PIG	88-99 271-282	4	A:29-40 B:29-40 A:212-223 B:212-223

(no "Exon" information available for 1PSA)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:326
 aligned with PEPA_PIG | P00791 from UniProtKB/Swiss-Prot  Length:385

    Alignment length:326
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379      
             PEPA_PIG    60 IGDEPLENYLDTEYFGTIGIGTPAQDFTVIFDTGSSNLWVPSVYCSSLACSDHNQFNPDDSSTFEATSQELSITYGTGSMTGILGYDTVQVGGISDTNQIFGLSETEPGSFLYYAPFDGILGLAYPSISASGATPVFDNLWDQGLVSQDLFSVYLSSNDDSGSVVLLGGIDSSYYTGSLNWVPVSVEGYWQITLDSITMDGETIACSGGCQAIVDTGTSLLTGPTSAIANIQSDIGASENSDGEMVISCSSIDSLPDIVFTINGVQYPLSPSAYILQDDDSCTSGFEGMDVPTSSGELWILGDVFIRQYYTVFDRANNKVGLAPVA 385
               SCOP domains d1psaa_ A: Pepsin(ogen)                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1psaA01 A:1-170 Acid Proteases                                                                                                                                            1psaA02 A:171-326 Acid Proteases                                                                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) .eeeee.........e.eeee.eeeeeeeeee....eeee.......hhhh.............e.....eeeee..eeeeeeeeeeeeee..eee..eeeeeeee...hhhhh...eeeeee............hhhhhhh......eeeeee........eeeeee.......e..eeeeee.....eeeeeeeeee..eeee...eeeeeee.....eee.hhhhhhhhhhh..eeee.eeeee.hhhhhh...eeeee..eeeee.hhhh----..eeeeeeeee.........eee.hhhhhh--------.eeeeeeee. Sec.struct. author (1)
     Sec.struct. author (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------eeeee-----------------------------eeeeeeeee---------- Sec.struct. author (2)
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------PEPTIDASE_A1  PDB: A:14-323 UniProt: 73-382                                                                                                                                                                                                                                                                           --- PROSITE (1)
                PROSITE (2) ----------------------------ASP_PROTEASE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1psa A   1 IGDEPLENYLDTEYFGTIGIGTPAQDFTVIFDTGSSNLWVPSVYCSSLACSDHNQFNPDDSSTFEATSQELSITYGTGSMTGILGYDTVQVGGISDTNQIFGLSETEPGSFLYYAPFDGILGLAYPSISASGATPVFDNLWDQGLVSQDLFSVYLSSNDDSGSVVLLGGIDSSYYTGSLNWVPVSVEGYWQITLDSITMDGETIACSGGCQAIVDTGTSLLTGPTSAIANIQSDIGASENSDGEMVISCSSIDSLPDIVFTINGVQYPLSPSAYILQDDDSCTSGFEGMDVPTSSGELWILGDVFIRQYYTVFDRANNKVGLAPVA 326
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320

Chain B from PDB  Type:PROTEIN  Length:326
 aligned with PEPA_PIG | P00791 from UniProtKB/Swiss-Prot  Length:385

    Alignment length:326
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379      
             PEPA_PIG    60 IGDEPLENYLDTEYFGTIGIGTPAQDFTVIFDTGSSNLWVPSVYCSSLACSDHNQFNPDDSSTFEATSQELSITYGTGSMTGILGYDTVQVGGISDTNQIFGLSETEPGSFLYYAPFDGILGLAYPSISASGATPVFDNLWDQGLVSQDLFSVYLSSNDDSGSVVLLGGIDSSYYTGSLNWVPVSVEGYWQITLDSITMDGETIACSGGCQAIVDTGTSLLTGPTSAIANIQSDIGASENSDGEMVISCSSIDSLPDIVFTINGVQYPLSPSAYILQDDDSCTSGFEGMDVPTSSGELWILGDVFIRQYYTVFDRANNKVGLAPVA 385
               SCOP domains d1psab_ B: Pepsin(ogen)                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1psaB01 B:1-170 Acid Proteases                                                                                                                                            1psaB02 B:171-326 Acid Proteases                                                                                                                             CATH domains
           Pfam domains (1) ------------Asp-1psaB01 B:13-325                                                                                                                                                                                                                                                                                                     - Pfam domains (1)
           Pfam domains (2) ------------Asp-1psaB02 B:13-325                                                                                                                                                                                                                                                                                                     - Pfam domains (2)
     Sec.struct. author (1) .eeeee.........e.eeee.eeeeeeeeee....eeee.......hhhh.............e.....eeeee..eeeeeeeeeeeeee..eee..eeeeeeee...hhhhh...eeeeee............hhhhhhh......eeeeee........eeeeee.......e..eeeeee.....eeeeeeeeee..eeee...eeeeeee.....eee.hhhhhhhhhhh..eeee.eeeee.hhhhhh...eeeee..eeeee.hhhh----..eeeeeeeee.........eee.hhhhhh--------.eeeeeeee. Sec.struct. author (1)
     Sec.struct. author (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------eeeee-----------------------------eeeeeeeee---------- Sec.struct. author (2)
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------PEPTIDASE_A1  PDB: B:14-323 UniProt: 73-382                                                                                                                                                                                                                                                                           --- PROSITE (1)
                PROSITE (2) ----------------------------ASP_PROTEASE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1psa B   1 IGDEPLENYLDTEYFGTIGIGTPAQDFTVIFDTGSSNLWVPSVYCSSLACSDHNQFNPDDSSTFEATSQELSITYGTGSMTGILGYDTVQVGGISDTNQIFGLSETEPGSFLYYAPFDGILGLAYPSISASGATPVFDNLWDQGLVSQDLFSVYLSSNDDSGSVVLLGGIDSSYYTGSLNWVPVSVEGYWQITLDSITMDGETIACSGGCQAIVDTGTSLLTGPTSAIANIQSDIGASENSDGEMVISCSSIDSLPDIVFTINGVQYPLSPSAYILQDDDSCTSGFEGMDVPTSSGELWILGDVFIRQYYTVFDRANNKVGLAPVA 326
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Acid proteases (1120)

Superfamily: Acid proteases (1120)

Family: Pepsin-like (505)

Protein domain: Pepsin(ogen) (16)

Pig (Sus scrofa) [TaxId: 9823] (8)

1a	d1psaa_	A:
1b	d1psab_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Cathepsin D, subunit A; domain 1 (745)

Homologous Superfamily: Acid Proteases (745)

Pig (Sus scrofa) (8)

1a	1psaA02	A:171-326
1b	1psaA01	A:1-170
1c	1psaB01	B:1-170
1d	1psaB02	B:171-326

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_AA (368)

Family: Asp (155)

Sus scrofa (Pig) (3)

1a	Asp-1psaB01	B:13-325
1b	Asp-1psaB02	B:13-325

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PEPA_PIG | P00791)

molecular function
	GO:0004190	aspartic-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
biological process
	GO:0007586	digestion	The whole of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.
	GO:0030163	protein catabolic process	The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Asymmetric/Biological Unit
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	1psa
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	PEPA_PIG \| P00791	:	1f34 1yx9 2psg 3pep 3psg 4pep 5pep

(no "Related Entries Specified in the PDB File" available for 1PSA)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

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SS Bonds (6, 6)

Cis Peptide Bonds (2, 2)

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