1AVF - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   ACTIVATION INTERMEDIATE 2 OF HUMAN GASTRICSIN FROM HUMAN STOMACH

Authors :   A. R. Khan, M. M. Cherney, N. I. Tarasova, M. N. G. James

Date :   16 Sep 97 (Deposition) - 25 Feb 98 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.36

Chains :   Asym. Unit : A,J,P,Q
Biol. Unit 1: A,P  (1x)
Biol. Unit 2: J,Q  (1x)

Keywords :   Aspartyl Protease, Gastricsin, Aspartic Proteinase, Intermediate, Activation, Acid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. R. Khan, M. M. Cherney, N. I. Tarasova, M. N. James
Structural Characterization Of Activation 'Intermediate 2' On The Pathway To Human Gastricsin.
Nat. Struct. Biol. V. 4 1010 1997
PubMed-ID: 9406551 | Reference-DOI: 10.1038/NSB1297-1010
(for further references see the PDB file header)

Molecule 1 - GASTRICSIN
	Chains	:	P, Q
	EC Number	:	3.4.23.3
	Organ	:	STOMACH
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	ASPARTIC PROTEINASE ACTIVATION INTERMEDIATE
	Synonym	:	PEPSINOGEN C
	Tissue	:	GASTRIC MUCOSA

Molecule 2 - GASTRICSIN
	Chains	:	A, J
	EC Number	:	3.4.23.3
	Organ	:	STOMACH
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	ASPARTIC PROTEINASE ACTIVATION INTERMEDIATE
	Synonym	:	PEPSINOGEN C
	Tissue	:	GASTRIC MUCOSA

		1	2	3	4
Asymmetric Unit	:	A	J	P	Q
Biological Unit 1 (1x)	:	A		P
Biological Unit 2 (1x)	:		J		Q

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	NA	1	Ligand/Ion	SODIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:275 , SER A:311 , HOH A:332 , HOH A:335 , HOH A:342 , HOH A:471	BINDING SITE FOR RESIDUE NA A 330

Asymmetric Unit

No.	Residues
1	A:45	-	A:50
2	A:208	-	A:212
3	A:251	-	A:284
4	J:45	-	J:50
5	J:208	-	J:212
6	J:251	-	J:284

Asymmetric Unit

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

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

Asymmetric Unit (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEPTIDASE_A1	PS51767	Peptidase family A1 domain profile.	PEPC_HUMAN	73-385	2	A:14-326 J:14-326
2	ASP_PROTEASE	PS00141	Eukaryotic and viral aspartyl proteases active site.	PEPC_HUMAN	88-99 273-284	4	A:29-40 J:29-40 A:214-225 J:214-225

Biological Unit 1 (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEPTIDASE_A1	PS51767	Peptidase family A1 domain profile.	PEPC_HUMAN	73-385	1	A:14-326 -
2	ASP_PROTEASE	PS00141	Eukaryotic and viral aspartyl proteases active site.	PEPC_HUMAN	88-99 273-284	2	A:29-40 - A:214-225 -

Biological Unit 2 (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEPTIDASE_A1	PS51767	Peptidase family A1 domain profile.	PEPC_HUMAN	73-385	1	- J:14-326
2	ASP_PROTEASE	PS00141	Eukaryotic and viral aspartyl proteases active site.	PEPC_HUMAN	88-99 273-284	2	- J:29-40 - J:214-225

Asymmetric Unit (9, 20)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2a	ENST00000373025	2a	ENSE00001958407	chr6:41715135-41715014	122	PEPC_HUMAN	1-20	20	2	- - P:1-4 Q:1-4	- - 4 4
1.3	ENST00000373025	3	ENSE00000750752	chr6:41712546-41712396	151	PEPC_HUMAN	20-70	51	4	A:2-11 J:2-11 P:4-21 Q:4-22	10 10 18 19
1.4c	ENST00000373025	4c	ENSE00002162675	chr6:41712252-41712135	118	PEPC_HUMAN	71-110	40	2	A:12-51 J:12-51 - -	40 40 - -
1.5	ENST00000373025	5	ENSE00002167075	chr6:41711127-41711009	119	PEPC_HUMAN	110-149	40	2	A:51-90 (gaps) J:51-90 - -	40 40 - -
1.6	ENST00000373025	6	ENSE00002151094	chr6:41710227-41710028	200	PEPC_HUMAN	150-216	67	2	A:91-157 J:91-157 - -	67 67 - -
1.9b	ENST00000373025	9b	ENSE00002190311	chr6:41708348-41708229	120	PEPC_HUMAN	216-256	41	2	A:157-197 (gaps) J:157-197 (gaps) - -	41 41 - -
1.10	ENST00000373025	10	ENSE00002152293	chr6:41707684-41707537	148	PEPC_HUMAN	256-305	50	2	A:197-246 J:197-246 - -	50 50 - -
1.11	ENST00000373025	11	ENSE00002188870	chr6:41705566-41705468	99	PEPC_HUMAN	306-338	33	2	A:247-279 J:247-279 - -	33 33 - -
1.12b	ENST00000373025	12b	ENSE00001814259	chr6:41704742-41704449	294	PEPC_HUMAN	339-388	50	2	A:280-329 J:280-329 - -	50 50 - -

Asymmetric 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:322
 aligned with PEPC_HUMAN | P20142 from UniProtKB/Swiss-Prot  Length:388

    Alignment length:328
                                    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       330       340       350       360       370       380        
           PEPC_HUMAN    61 VTYEPMAYMDAAYFGEISIGTPPQNFLVLFDTGSSNLWVPSVYCQSQACTSHSRFNPSESSTYSTNGQTFSLQYGSGSLTGFFGYDTLTVQSIQVPNQEFGLSENEPGTNFVYAQFDGIMGLAYPALSVDEATTAMQGMVQEGALTSPVFSVYLSNQQGSSGGAVVFGGVDSSLYTGQIYWAPVTQELYWQIGIEEFLIGGQASGWCSEGCQAIVDTGTSLLTVPQQYMSALLQATGAQEDEYGQFLVNCNSIQNLPSLTFIINGVEFPLPPSSYILSNNGYCTVGVEPTYLSSQNGQPLWILGDVFLRSYYSVYDLGNNRVGFATAA 388
               SCOP domains d1avf.1 P:,A: Pepsin(ogen)                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1avfA01 A:2-171 Acid Proteases                                                                                                                                            1avfA02 A:172-327 Acid Proteases                                                                                                                            -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeee....eeeeeeee......eee......hhhh......hhh.........eeee..-...eeeeeeee.eee..eee..eeeeee.....hhhhh....eeee...hhh.hhh...hhhhhhhh......eeeee...-----..eeee............eeee.......eeee.eeee...........eeeee......eeeehhhhhhhhhh.................hhh...eeeee..eee...hhhheee....eee.eeee.........eeee.hhhh..eeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------PEPTIDASE_A1  PDB: A:14-326 UniProt: 73-385                                                                                                                                                                                                                                                                              --- PROSITE (1)
                PROSITE (2) ---------------------------ASP_PROTEASE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE-------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) ----------Exon 1.4c  PDB: A:12-51 UniProt: 71-110 ---------------------------------------Exon 1.6  PDB: A:91-157 UniProt: 150-216                           ---------------------------------------Exon 1.10  PDB: A:197-246 UniProt: 256-305        Exon 1.11  PDB: A:247-279        Exon 1.12b  PDB: A:280-329 UniProt: 339-388        Transcript 1 (1)
           Transcript 1 (2) Exon 1.3  ---------------------------------------Exon 1.5  PDB: A:51-90 (gaps)           ------------------------------------------------------------------Exon 1.9b  PDB: A:157-197 (gaps)         ------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 1avf A   2 VTYEPMAYMDAAYFGEISIGTPPQNFLVLFDTGSSNLWVPSVYCQSQACTSHSRFNPSESSTYSTNGQTFSLQY-SGSLTGFFGYDTLTVQSIQVPNQEFGLSENEPGTNFVYAQFDGIMGLAYPALSVDEATTAMQGMVQEGALTSPVFSVYLSN-----GGAVVFGGVDSSLYTGQIYWAPVTQELYWQIGIEEFLIGGQASGWCSEGCQAIVDTGTSLLTVPQQYMSALLQATGAQEDEYGQFLVNCNSIQNLPSLTFIINGVEFPLPPSSYILSNNGYCTVGVEPTYLSSQNGQPLWILGDVFLRSYYSVYDLGNNRVGFATAA 329
                                    11        21        31        41        51        61        71   | |  81        91       101       111       121       131       141       151     |   - |     171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321        
                                                                                                    75 |                                                                             157   163                                                                                                                                                                      
                                                                                                      77

Chain J from PDB  Type:PROTEIN  Length:323
 aligned with PEPC_HUMAN | P20142 from UniProtKB/Swiss-Prot  Length:388

    Alignment length:328
                                    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       330       340       350       360       370       380        
           PEPC_HUMAN    61 VTYEPMAYMDAAYFGEISIGTPPQNFLVLFDTGSSNLWVPSVYCQSQACTSHSRFNPSESSTYSTNGQTFSLQYGSGSLTGFFGYDTLTVQSIQVPNQEFGLSENEPGTNFVYAQFDGIMGLAYPALSVDEATTAMQGMVQEGALTSPVFSVYLSNQQGSSGGAVVFGGVDSSLYTGQIYWAPVTQELYWQIGIEEFLIGGQASGWCSEGCQAIVDTGTSLLTVPQQYMSALLQATGAQEDEYGQFLVNCNSIQNLPSLTFIINGVEFPLPPSSYILSNNGYCTVGVEPTYLSSQNGQPLWILGDVFLRSYYSVYDLGNNRVGFATAA 388
               SCOP domains d1avf.2 Q:,J: Pepsin(ogen)                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1avfJ01 J:2-171 Acid Proteases                                                                                                                                            1avfJ02 J:172-328 Acid Proteases                                                                                                                             - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeee....eeeeeeee......eee......hhhh......hhh.........eee........eeeeeee.eee..eee..eeeeee.....hhhhh....eeee...hhh.hhh...hhhhhhh.......eeeee...-----..eeee....hhh.....eeee.......eeee.eeee...........eeeee......eeeehhhhhhhhhhh.............hhhhhh...eeeee..eeeee.hhhheee....eee.eeee........eeeee.hhhh..eeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------PEPTIDASE_A1  PDB: J:14-326 UniProt: 73-385                                                                                                                                                                                                                                                                              --- PROSITE (1)
                PROSITE (2) ---------------------------ASP_PROTEASE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE-------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) ----------Exon 1.4c  PDB: J:12-51 UniProt: 71-110 ---------------------------------------Exon 1.6  PDB: J:91-157 UniProt: 150-216                           ---------------------------------------Exon 1.10  PDB: J:197-246 UniProt: 256-305        Exon 1.11  PDB: J:247-279        Exon 1.12b  PDB: J:280-329 UniProt: 339-388        Transcript 1 (1)
           Transcript 1 (2) Exon 1.3  ---------------------------------------Exon 1.5  PDB: J:51-90 UniProt: 110-149 ------------------------------------------------------------------Exon 1.9b  PDB: J:157-197 (gaps)         ------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 1avf J   2 VTYEPMAYMDAAYFGEISIGTPPQNFLVLFDTGSSNLWVPSVYCQSQACTSHSRFNPSESSTYSTNGQTFSLQYGSGSLTGFFGYDTLTVQSIQVPNQEFGLSENEPGTNFVYAQFDGIMGLAYPALSVDEATTAMQGMVQEGALTSPVFSVYLSN-----GGAVVFGGVDSSLYTGQIYWAPVTQELYWQIGIEEFLIGGQASGWCSEGCQAIVDTGTSLLTVPQQYMSALLQATGAQEDEYGQFLVNCNSIQNLPSLTFIINGVEFPLPPSSYILSNNGYCTVGVEPTYLSSQNGQPLWILGDVFLRSYYSVYDLGNNRVGFATAA 329
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151     |   - |     171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321        
                                                                                                                                                                                     157   163

Chain P from PDB  Type:PROTEIN  Length:21
 aligned with PEPC_HUMAN | P20142 from UniProtKB/Swiss-Prot  Length:388

    Alignment length:21
                                    26        36 
           PEPC_HUMAN    17 AVVKVPLKKFKSIRETMKEKG  37
               SCOP domains d1avf.1 P:,A:         SCOP domains
               CATH domains --------------------- CATH domains
               Pfam domains --------------------- Pfam domains
         Sec.struct. author ............hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------- SAPs(SNPs)
                PROSITE (1) --------------------- PROSITE (1)
                PROSITE (2) --------------------- PROSITE (2)
           Transcript 1 (1) 1.2a----------------- Transcript 1 (1)
           Transcript 1 (2) ---Exon 1.3           Transcript 1 (2)
                 1avf P   1 AVVKVPLKKFKSIRETMKEKG  21
                                    10        20

Chain Q from PDB  Type:PROTEIN  Length:22
 aligned with PEPC_HUMAN | P20142 from UniProtKB/Swiss-Prot  Length:388

    Alignment length:22
                                    26        36  
           PEPC_HUMAN    17 AVVKVPLKKFKSIRETMKEKGL  38
               SCOP domains d1avf.2 Q:,J:          SCOP domains
               CATH domains ---------------------- CATH domains
               Pfam domains ---------------------- Pfam domains
         Sec.struct. author ............hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------- SAPs(SNPs)
                PROSITE (1) ---------------------- PROSITE (1)
                PROSITE (2) ---------------------- PROSITE (2)
           Transcript 1 (1) 1.2a------------------ Transcript 1 (1)
           Transcript 1 (2) ---Exon 1.3            Transcript 1 (2)
                 1avf Q   1 AVVKVPLKKFKSIRETMKEKGL  22
                                    10        20

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 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)

Human (Homo sapiens), progastricsin (pepsinogen C) [TaxId: 9606] (2)

1a	d1avf.1	P:,A:
1b	d1avf.2	Q:,J:

Asymmetric 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)

Human (Homo sapiens) (161)

1a	1avfA02	A:172-327
1b	1avfJ02	J:172-328
1c	1avfA01	A:2-171
1d	1avfJ01	J:2-171

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

Asymmetric Unit(hide GO term definitions)

Chain A,J,P,Q (PEPC_HUMAN | P20142)

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:0002803	positive regulation of antibacterial peptide production	Any process that activates or increases the frequency, rate, or extent of antibacterial peptide production.
	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:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	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.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

Asymmetric Unit
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Access by PDB/NDB ID
	1avf
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	PEPC_HUMAN \| P20142	:	1htr

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

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 (9, 20)

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