2WEC - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   ACID PROTEINASE (PENICILLOPEPSIN) (E.C.3.4.23.20) COMPLEX WITH PHOSPHONATE INHIBITOR: METHYL(2S)-[1-(((N-(1-NAPHTHALENEACETYL))-L-VALYL)AMINOMETHYL)HYDROXY PHOSPHINYLOXY]-3-PHENYLPROPANOATE, SODIUM SALT

Authors :   J. Ding, M. E. Fraser, M. N. G. James

Date :   03 Feb 98 (Deposition) - 27 May 98 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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

Keywords :   Penicillopepsin, Phosphonate Inhibitor, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Ding, M. E. Fraser, J. H. Meyer, P. A. Bartlett, M. N. G. James
Macrocyclic Inhibitors Of Penicillopepsin. Ii. X-Ray Crystallographic Analyses Of Penicillopepsin Complexed With A P3-P1 Macrocyclic Peptidyl Inhibitor And With Its Two Acyclic Analogues
J. Am. Chem. Soc. V. 120 4610 1998
PubMed: search
(for further references see the PDB file header)

Molecule 1 - PENICILLOPEPSIN
	Chains	:	A
	EC Number	:	3.4.23.20
	Organism Scientific	:	PENICILLIUM JANTHINELLUM
	Organism Taxid	:	5079

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 4)

No.	Name	Count	Type	Full Name
1	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE
2	PP5	1	Ligand/Ion	METHYL (2S)-[1-((N-(NAPHTHALENEACETYL))-L-VALYL)AMINOMETHYL)HYDROXYPHOSPHINYLOXY]-3-PHENYL PROPANOATE
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 8)

No.	Name	Count	Type	Full Name
1	MAN	4	Ligand/Ion	ALPHA-D-MANNOSE
2	PP5	2	Ligand/Ion	METHYL (2S)-[1-((N-(NAPHTHALENEACETYL))-L-VALYL)AMINOMETHYL)HYDROXYPHOSPHINYLOXY]-3-PHENYL PROPANOATE
3	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:3 , THR A:9 , PRO A:10 , THR A:11 , GLN A:160 , GLN A:161 , PRO A:162 , HOH A:385 , HOH A:523 , HOH A:542 , HOH A:572	BINDING SITE FOR RESIDUE MAN A 324
2	AC2	SOFTWARE	THR A:7 , GLN A:150 , HOH A:495 , HOH A:577 , HOH A:595 , HOH A:675	BINDING SITE FOR RESIDUE MAN A 325
3	AC3	SOFTWARE	TYR A:175 , SER A:178 , LEU A:179 , HOH A:608	BINDING SITE FOR RESIDUE SO4 A 339
4	AC4	SOFTWARE	GLU A:15 , TYR A:75 , GLY A:76 , ASP A:77 , ASP A:213 , GLY A:215 , THR A:216 , THR A:217 , LEU A:218 , ALA A:242 , GLY A:243 , HOH A:364 , HOH A:389 , HOH A:442 , HOH A:651 , HOH A:663	BINDING SITE FOR RESIDUE PP5 A 326
5	CIC	UNKNOWN	ASP A:33 , ASP A:213	CATALYTIC SITE.

Asymmetric Unit

No.	Residues
1	A:249	-	A:283

Asymmetric Unit

No.	Residues
1	Gln A:133	-	Pro A:134
2	Gly A:314	-	Pro A:315

(no "SAP(SNP)/Variant" information available for 2WEC)

Asymmetric Unit (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEPTIDASE_A1	PS51767	Peptidase family A1 domain profile.	PEPA1_PENJA	17-320	1	A:17-320
2	ASP_PROTEASE	PS00141	Eukaryotic and viral aspartyl proteases active site.	PEPA1_PENJA	30-41 210-221	2	A:30-41 A:210-221

Biological Unit 1 (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEPTIDASE_A1	PS51767	Peptidase family A1 domain profile.	PEPA1_PENJA	17-320	2	A:17-320
2	ASP_PROTEASE	PS00141	Eukaryotic and viral aspartyl proteases active site.	PEPA1_PENJA	30-41 210-221	4	A:30-41 A:210-221

(no "Exon" information available for 2WEC)

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:323
 aligned with PEPA1_PENJA | P00798 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:323
                                    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   
          PEPA1_PENJA     1 AASGVATNTPTANDEEYITPVTIGGTTLNLNFDTGSADLWVFSTELPASQQSGHSVYNPSATGKELSGYTWSISYGDGSSASGNVFTDSVTVGGVTAHGQAVQAAQQISAQFQQDTNNDGLLGLAFSSINTVQPQSQTTFFDTVKSSLAQPLFAVALKHQQPGVYDFGFIDSSKYTGSLTYTGVDNSQGFWSFNVDSYTAGSQSGDGFSGIADTGTTLLLLDDSVVSQYYSQVSGAQQDSNAGGYVFDCSTNLPDFSVSISGYTATVPGSLINYGPSGDGSTCLGGIQSNSGIGFSIFGDIFLKSQYVVFDSDGPQLGFAPQA 323
               SCOP domains d2weca_ A: Acid protease                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains -----2wecA01 A:6-170 Acid Proteases                                                                                                                                       2wecA02 A:171-322 Acid Proteases                                                                                                                        - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhh...eeeeee..eeeeeeee.....eee......hhhh.......hhhh.......eeeee.....eeeeeeeee.eee..eee..eeeeeeeee.hhhhh.....eeee...hhh..........hhhhhhhh....eeeee.......eeee....hhh.....eeee........eeee.eeee..eeee.eeeee......eee.hhhhhhhhhh....eee....eeeee.......eeeee..eeeee.hhhheeee.....eeee.eee......eee.hhhhhheeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------PEPTIDASE_A1  PDB: A:17-320 UniProt: 17-320                                                                                                                                                                                                                                                                     --- PROSITE (1)
                PROSITE (2) -----------------------------ASP_PROTEASE------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wec A   1 AASGVATNTPTANDEEYITPVTIGGTTLNLNFDTGSADLWVFSTELPASQQSGHSVYNPSATGKELSGYTWSISYGDGSSASGNVFTDSVTVGGVTAHGQAVQAAQQISAQFQQDTNNDGLLGLAFSSINTVQPQSQTTFFDTVKSSLAQPLFAVALKHQQPGVYDFGFIDSSKYTGSLTYTGVDNSQGFWSFNVDSYTAGSQSGDGFSGIADTGTTLLLLDDSVVSQYYSQVSGAQQDSNAGGYVFDCSTNLPDFSVSISGYTATVPGSLINYGPSGDGSTCLGGIQSNSGIGFSIFGDIFLKSQYVVFDSDGPQLGFAPQA 323
                                    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(

)

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 (Penicillium janthinellum), penicillopepsin [TaxId: 5079] (14)

d2weca_

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)

Penicillium janthinellum. Organism_taxid: 5079 (7)

1a	2wecA02	A:171-322
1b	2wecA01	A:6-170

(no "Pfam Domain" information available for 2WEC)

Asymmetric Unit(hide GO term definitions)

Chain A (PEPA1_PENJA | P00798)

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.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		MAN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PP5	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		CIC	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gln A:133 - Pro A:134	[ RasMol ]
		Gly A:314 - Pro A:315	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2wec
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	PEPA1_PENJA \| P00798
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.4.23.20
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	PEPA1_PENJA \| P00798
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	PEPA1_PENJA \| P00798	:	1apt 1apu 1apv 1apw 1bxo 1bxq 1ppk 1ppl 1ppm 2wea 2web 2wed 3app

(no "Related Entries Specified in the PDB File" available for 2WEC)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (5, 5)

SS Bonds (1, 1)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 3)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (4, 4)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File