1F34 - JenaLib

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Title :   CRYSTAL STRUCTURE OF ASCARIS PEPSIN INHIBITOR-3 BOUND TO PORCINE PEPSIN

Authors :   K. K. Ng, J. F. Petersen, M. M. Cherney, C. Garen, M. N. James

Date :   31 May 00 (Deposition) - 01 Feb 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.45

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

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

Reference :   K. K. Ng, J. F. Petersen, M. M. Cherney, C. Garen, J. J. Zalatoris, C. Rao-Naik, B. M. Dunn, M. R. Martzen, R. J. Peanasky, M. N. James
Structural Basis For The Inhibition Of Porcine Pepsin By Ascaris Pepsin Inhibitor-3.
Nat. Struct. Biol. V. 7 653 2000
PubMed-ID: 10932249 | Reference-DOI: 10.1038/77950
(for further references see the PDB file header)

Molecule 1 - PEPSIN A
	Chains	:	A
	EC Number	:	3.4.23.1
	Organ	:	STOMACH
	Organism Common	:	PIG
	Organism Scientific	:	SUS SCROFA
	Organism Taxid	:	9823

Molecule 2 - MAJOR PEPSIN INHIBITOR PI-3
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-3D
	Expression System Taxid	:	562
	Organism Common	:	PIG ROUNDWORM
	Organism Scientific	:	ASCARIS SUUM
	Organism Taxid	:	6253

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
2	SEP	1	Mod. Amino Acid	PHOSPHOSERINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:75 , THR A:77 , GLY A:78 , LEU A:112 , ILE A:120	BINDING SITE FOR RESIDUE MPD A 327

Asymmetric/Biological Unit

No.	Residues
1	A:45	-	A:50
2	A:206	-	A:210
3	A:249	-	A:282
4	B:13	-	B:66
5	B:48	-	B:59
6	B:79	-	B:146

Asymmetric/Biological Unit

No.	Residues
1	Thr A:22	-	Pro A:23
2	Gly B:9	-	Pro B:10

(no "SAP(SNP)/Variant" information available for 1F34)

Asymmetric/Biological Unit (2, 3)

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

(no "Exon" information available for 1F34)

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 d1f34a_ A: Pepsin(ogen)                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1f34A01 A:1-170 Acid Proteases                                                                                                                                            1f34A02 A:171-325 Acid Proteases                                                                                                                           - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.eee...eeeeeeee....eeeeeeee.....eeee.....hhhhhhh...hhhhh...eeeeeeeeeee...eeeeeeeeeeeee..eeeeeeeeeeeee..hhhhhhh...eeee..hhhhhhhhh.hhhhhhhhh......eeeee.........eeee...hhhh.....eeee.......eeee.eeee..eeee....eeeee......eeehhhhhhhhhhh...ee.....ee...hhhhh...eeeee..eeeee.....eee....eee.eee...ee..ee.eeehhhhhh.eeeeee....eeeeee.. Sec.struct. author
                 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
                 1f34 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      
                                                                                              68-SEP

Chain B from PDB  Type:PROTEIN  Length:138
 aligned with API3_ASCSU | P19400 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:148
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160        
           API3_ASCSU    21 QFLFSMSTGPFICTVKDNQVFVANLPWTMLEGDDIQVGKEFAARVEDCTNVKHDMAPTCTKPPPFCGPQDMKMFNFVGCSVLGNKLFIDQKYVRDLTAKDHAEVQTFREKIAAFEEQQENQPPSSGMPHGAVPAGGLSPPPPPSFCTV 168
               SCOP domains d1f34b_ B: Pepsin inhibitor-3                                                                                                                        SCOP domains
               CATH domains 1f34B01  ------------------------------------------------------------1f34B01 B:1-9,B:70-148 Pepsin inhibitor-3                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....eeee..eeee..eeeee.hhhhhhhhhhhhhhhhhhhhh....hhhhhh.hhhhh....eeeee..eeee..eeee...eeee.hhhhhhhhhhhhhhhhhhhhhhh...----------..........hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f34 B   1 QFLFSMSTGPFICTVKDNQVFVANLPWTMLEGDDIQVGKEFAARVEDCTNVKHDMAPTCTKPPPFCGPQDMKMFNFVGCSVLGNKLFIDQKYVRDLTAKDHAEVQTFREKIAAFEEQQENQP----------PAGGLSPPPPPSFCTV 148
                                    10        20        30        40        50        60        70        80        90       100       110       120 |       -  |    140        
                                                                                                                                                   122        133

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)

d1f34a_

Class: Alpha and beta proteins (a+b) (23004)

Fold: Pepsin inhibitor-3 (2)

Superfamily: Pepsin inhibitor-3 (2)

Family: Pepsin inhibitor-3 (2)

Protein domain: Pepsin inhibitor-3 (2)

Pig roundworm (Ascaris suum) [TaxId: 6253] (2)

d1f34b_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Arylsulfatase, C-terminal domain (26)

Homologous Superfamily: Pepsin inhibitor-3 (2)

Pig (Sus scrofa) (1)

1f34B01

B:1-9,B:70-148

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)

2a	1f34A02	A:171-325
2b	1f34A01	A:1-170

(no "Pfam Domain" information available for 1F34)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (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.

Chain B (API3_ASCSU | P19400)

molecular function
	GO:0019828	aspartic-type endopeptidase inhibitor activity	Stops, prevents or reduces the activity of aspartic-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; the optimum reaction pH is below 5 due to an aspartic residue involved in the catalytic process.
	GO:0030414	peptidase inhibitor activity	Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
biological process
	GO:0010951	negative regulation of endopeptidase activity	Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
	GO:0010466	negative regulation of peptidase activity	Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
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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UniProtKB/Swiss-Prot
	API3_ASCSU \| P19400	:	1f32
	PEPA_PIG \| P00791	:	1psa 1yx9 2psg 3pep 3psg 4pep 5pep

1f32	ASCARIS PEPSIN INHIBITOR-3

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (1, 1)

SS Bonds (6, 6)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File