1IBQ - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   ASPERGILLOPEPSIN FROM ASPERGILLUS PHOENICIS

Authors :   S. W. Cho, W. Shin

Date :   28 Mar 01 (Deposition) - 04 Jul 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.14

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Aspergillopepsin, Aspartic Proteinase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. W. Cho, N. Kim, M. U. Choi, W. Shin
Structure Of Aspergillopepsin I From Aspergillus Phoenicis: Variations Of The S1'-S2 Subsite In Aspartic Proteinases.
Acta Crystallogr. , Sect. D V. 57 948 2001
PubMed-ID: 11418762 | Reference-DOI: 10.1107/S0907444901005972
(for further references see the PDB file header)

Molecule 1 - ASPERGILLOPEPSIN
	Chains	:	A, B
	EC Number	:	3.4.23.18
	Organism Scientific	:	ASPERGILLUS PHOENICIS
	Organism Taxid	:	5063

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 12)

No.	Name	Count	Type	Full Name
1	MAN	4	Ligand/Ion	ALPHA-D-MANNOSE
2	ZN	8	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SER A:235 , HOH A:1114 , HOH A:1199 , HOH A:1237	BINDING SITE FOR RESIDUE MAN A 435
02	AC2	SOFTWARE	SER A:59 , SER A:60 , HOH A:1134	BINDING SITE FOR RESIDUE MAN A 460
03	AC3	SOFTWARE	SER B:235 , HOH B:1110	BINDING SITE FOR RESIDUE MAN B 935
04	AC4	SOFTWARE	GLY B:23 , LYS B:24 , SER B:59 , SER B:60	BINDING SITE FOR RESIDUE MAN B 960
05	AC5	SOFTWARE	SER A:1 , ASP A:148	BINDING SITE FOR RESIDUE ZN A 1451
06	AC6	SOFTWARE	HIS B:28 , ASP B:54 , ALA B:116 , ASP B:118 , HOH B:1120 , HOH B:1167	BINDING SITE FOR RESIDUE ZN B 1452
07	AC7	SOFTWARE	ASP A:256	BINDING SITE FOR RESIDUE ZN A 1453
08	AC8	SOFTWARE	SER B:1 , ASP B:148 , HOH B:1006	BINDING SITE FOR RESIDUE ZN B 1454
09	AC9	SOFTWARE	HIS A:28 , ASP A:54 , ASP A:118	BINDING SITE FOR RESIDUE ZN A 1455
10	BC1	SOFTWARE	GLU B:232	BINDING SITE FOR RESIDUE ZN B 1456
11	BC2	SOFTWARE	ASP A:32 , GLY A:34 , ASP A:214 , HOH A:1046 , HOH A:1122	BINDING SITE FOR RESIDUE ZN A 1457
12	BC3	SOFTWARE	ASP B:32 , GLY B:34 , ASP B:214 , HOH B:1214	BINDING SITE FOR RESIDUE ZN B 1458

Asymmetric Unit

No.	Residues
1	A:250	-	A:285
2	B:250	-	B:285

Asymmetric Unit

No.	Residues
1	Gln A:132	-	Pro A:133
2	Gly A:316	-	Pro A:317
3	Gln B:132	-	Pro B:133
4	Gly B:316	-	Pro B:317

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

Asymmetric Unit (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEPTIDASE_A1	PS51767	Peptidase family A1 domain profile.	PEPA_ASPPH	85-391	2	A:16-322 B:16-322
2	ASP_PROTEASE	PS00141	Eukaryotic and viral aspartyl proteases active site.	PEPA_ASPPH	98-109 280-291	4	A:29-40 B:29-40 A:211-222 B:211-222

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.	PEPA_ASPPH	85-391	1	A:16-322 -
2	ASP_PROTEASE	PS00141	Eukaryotic and viral aspartyl proteases active site.	PEPA_ASPPH	98-109 280-291	2	A:29-40 - A:211-222 -

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.	PEPA_ASPPH	85-391	1	- B:16-322
2	ASP_PROTEASE	PS00141	Eukaryotic and viral aspartyl proteases active site.	PEPA_ASPPH	98-109 280-291	2	- B:29-40 - B:211-222

(no "Exon" information available for 1IBQ)

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:325
 aligned with PEPA_ASPPH | Q12567 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:325
                                    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       389     
           PEPA_ASPPH    70 SKGSAVTTPQNNDEEYLTPVTVGKSTLHLDFDTGSADLWVFSDELPSSEQTGHDLYTPSSSATKLSGYSWDISYGDGSSASGDVYRDTVTVGGVTTNKQAVEAASKISSEFVQDTANDGLLGLAFSSINTVQPKAQTTFFDTVKSQLDSPLFAVQLKHDAPGVYDFGYIDDSKYTGSITYTDADSSQGYWGFSTDGYSIGDGSSSSSGFSAIADTGTTLILLDDEIVSAYYEQVSGAQESYEAGGYVFSCSTDLPDFTVVIGDYKAVVPGKYINYAPVSTGSSTCYGGIQSNSGLGLSILGDVFLKSQYVVFNSEGPKLGFAAQA 394
               SCOP domains d1ibqa_ A: Acid protease                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----1ibqA01 A:5-169 Acid Proteases                                                                                                                                       1ibqA02 A:170-324 Acid Proteases                                                                                                                           - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee......eeeeeee..eeeeeeee.....eeee....hhhhhh...........ee.....eeee.....eeeeeeeeeeeee..eeeeeeeeeeeeeehhhhhh.....eeee..hhhhh........hhhhhhhhhh...eeeeeee..eeeeeee...hhhh.....eeee........eeee.eeee.........eeeee......eeehhhhhhhhhh..............eee.......eeeee..eeeeehhhhheeee......eeee.eee......eeehhhhhh.eeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------PEPTIDASE_A1  PDB: A:16-322 UniProt: 85-391                                                                                                                                                                                                                                                                        --- PROSITE (1)
                PROSITE (2) ----------------------------ASP_PROTEASE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ibq A   1 SKGSAVTTPQNNDEEYLTPVTVGKSTLHLDFDTGSADLWVFSDELPSSEQTGHDLYTPSSSATKLSGYSWDISYGDGSSASGDVYRDTVTVGGVTTNKQAVEAASKISSEFVQDTANDGLLGLAFSSINTVQPKAQTTFFDTVKSQLDSPLFAVQLKHDAPGVYDFGYIDDSKYTGSITYTDADSSQGYWGFSTDGYSIGDGSSSSSGFSAIADTGTTLILLDDEIVSAYYEQVSGAQESYEAGGYVFSCSTDLPDFTVVIGDYKAVVPGKYINYAPVSTGSSTCYGGIQSNSGLGLSILGDVFLKSQYVVFNSEGPKLGFAAQA 325
                                    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:325
 aligned with PEPA_ASPPH | Q12567 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:325
                                    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       389     
           PEPA_ASPPH    70 SKGSAVTTPQNNDEEYLTPVTVGKSTLHLDFDTGSADLWVFSDELPSSEQTGHDLYTPSSSATKLSGYSWDISYGDGSSASGDVYRDTVTVGGVTTNKQAVEAASKISSEFVQDTANDGLLGLAFSSINTVQPKAQTTFFDTVKSQLDSPLFAVQLKHDAPGVYDFGYIDDSKYTGSITYTDADSSQGYWGFSTDGYSIGDGSSSSSGFSAIADTGTTLILLDDEIVSAYYEQVSGAQESYEAGGYVFSCSTDLPDFTVVIGDYKAVVPGKYINYAPVSTGSSTCYGGIQSNSGLGLSILGDVFLKSQYVVFNSEGPKLGFAAQA 394
               SCOP domains d1ibqb_ B: Acid protease                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----1ibqB01 B:5-169 Acid Proteases                                                                                                                                       1ibqB02 B:170-324 Acid Proteases                                                                                                                           - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.........eeeeee..eeeeeeee.....eee.....hhhhh............ee.....ee........eeeeeeeeeeee..eeeeeeeeeeeeeehhhhhhh....eeee..hhhhh........hhhhhhhhhh...eeeeeee..eeeeeee............eeee........eeee.eeee.........eeeee......eeehhhhhhhhhh.....eee....eeeee.......eeeee..eeeeehhhhheeee......eeee.eee......eee...hhh.eeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------PEPTIDASE_A1  PDB: B:16-322 UniProt: 85-391                                                                                                                                                                                                                                                                        --- PROSITE (1)
                PROSITE (2) ----------------------------ASP_PROTEASE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ibq B   1 SKGSAVTTPQNNDEEYLTPVTVGKSTLHLDFDTGSADLWVFSDELPSSEQTGHDLYTPSSSATKLSGYSWDISYGDGSSASGDVYRDTVTVGGVTTNKQAVEAASKISSEFVQDTANDGLLGLAFSSINTVQPKAQTTFFDTVKSQLDSPLFAVQLKHDAPGVYDFGYIDDSKYTGSITYTDADSSQGYWGFSTDGYSIGDGSSSSSGFSAIADTGTTLILLDDEIVSAYYEQVSGAQESYEAGGYVFSCSTDLPDFTVVIGDYKAVVPGKYINYAPVSTGSSTCYGGIQSNSGLGLSILGDVFLKSQYVVFNSEGPKLGFAAQA 325
                                    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 Unit

Classes(

)

Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Acid proteases (1120)

Superfamily: Acid proteases (1120)

Family: Pepsin-like (505)

Protein domain: Acid protease (44)

Fungus (Aspergillus phoenicis), aspergillopepsin [TaxId: 5063] (1)

1a	d1ibqa_	A:
1b	d1ibqb_	B:

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)

Aspergillus phoenicis. Organism_taxid: 5063 (1)

1a	1ibqA02	A:170-324
1b	1ibqB02	B:170-324
1c	1ibqA01	A:5-169
1d	1ibqB01	B:5-169

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (PEPA_ASPPH | Q12567)

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: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 Unit
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	Cis Peptide Bonds
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		Gln B:132 - Pro B:133	[ RasMol ]
		Gly A:316 - Pro A:317	[ RasMol ]
		Gly B:316 - Pro B:317	[ RasMol ]

Biological Units
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(no "Entries Sharing at Least One Protein Chain" available for 1IBQ)

1eag	1EAG CONTAINS ASPARTIC PROTEINASE (SAP2) FROM CANDIDA ALBICANS.
1mpp	1MPP CONTAINS PEPSIN (RENIN).
1psn	1PSN CONTAINS PEPSIN 3A.
2apr	2APR CONTAINS ACID PROTEINASE (RHIZOPUSPEPSIN).
3app	3APP CONTAINS ACID PROTEINASE (PENICILLOPEPSIN).
4ape	4APE CONTAINS ACID PROTEINASE (ENDOTHIAPEPSIN).

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (2, 12)

Sites (12, 12)

SS Bonds (2, 2)

Cis Peptide Bonds (4, 4)

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SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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