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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   ENDOTHIAPEPSIN COMPLEXED WITH H256

Authors :   L. Coates, P. T. Erskine, M. P. Crump, S. P. Wood, J. B. Cooper

Date :   27 Feb 02 (Deposition) - 04 Jul 02 (Release) - 21 Dec 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.00

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

Keywords :   Hydrolase, Aspartic Proteinase Mechanism, Tetrahedral Intermediate, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Coates, P. T. Erskine, M. P. Crump, S. P. Wood, J. B. Cooper
Five Atomic Resolution Structures Of Endothiapepsin Inhibitor Complexes: Implications For The Aspartic Proteinase Mechanism
J. Mol. Biol. V. 318 1405 2002
PubMed-ID: 12083527 | Reference-DOI: 10.1016/S0022-2836(02)00197-3

Molecule 1 - ENDOTHIAPEPSIN
	Chains	:	A
	EC Number	:	3.4.23.22
	Organism Common	:	CHESTNUT BLIGHT FUNGUS
	Organism Scientific	:	ENDOTHIA PARASITICA
	Organism Taxid	:	5116
	Synonym	:	ASPARTATE PROTEASE

Molecule 2 - INHIBITOR H256
	Chains	:	I
	Engineered	:	YES
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630
	Synthetic	:	YES

		1	2
Asymmetric/Biological Unit	:	A	I

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 4)

No.	Name	Count	Type	Full Name
1	PUK	1	Mod. Amino Acid	N-[(2S)-2-AMINO-3-PHENYLPROPYL]-L-PHENYLALANINE
2	SO4	2	Ligand/Ion	SULFATE ION
3	SUI	1	Mod. Amino Acid	(3-AMINO-2,5-DIOXO-1-PYRROLIDINYL)ACETIC ACID

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:113 , SER A:114 , THR A:322 , HOH A:2175 , HOH A:2389 , HOH A:2390 , HOH A:2391 , HOH A:2392	BINDING SITE FOR RESIDUE SO4 A 501
2	AC2	SOFTWARE	LYS A:243 , SER A:245 , SER A:246 , SER A:247 , HOH A:2393 , HOH A:2394	BINDING SITE FOR RESIDUE SO4 A 502
3	AC3	SOFTWARE	ASP A:15 , ASP A:33 , ASP A:35 , GLY A:37 , SER A:78 , TYR A:79 , GLY A:80 , ASP A:81 , SER A:83 , LEU A:133 , ASP A:219 , GLY A:221 , THR A:222 , THR A:223 , HOH A:2060 , HOH A:2372 , HOH I:2001 , HOH I:2002 , HOH I:2003 , HOH I:2004	BINDING SITE FOR CHAIN I OF INHIBITOR H256

Asymmetric/Biological Unit

No.	Residues
1	A:255	-	A:290

Asymmetric/Biological Unit

No.	Residues
1	Thr A:25	-	Pro A:26
2	Ser A:137	-	Pro A:138

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

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.	CARP_CRYPA	106-417	1	A:17-328
2	ASP_PROTEASE	PS00141	Eukaryotic and viral aspartyl proteases active site.	CARP_CRYPA	121-132 305-316	2	A:32-43 A:216-227

(no "Exon" information available for 1GVX)

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:329
 aligned with CARP_CRYPA | P11838 from UniProtKB/Swiss-Prot  Length:419

    Alignment length:330
                                    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       399       409       419
           CARP_CRYPA    90 STGSATTTPIDSLDDAYITPVQIGTPAQTLNLDFDTGSSDLWVFSSETTASEVDGQTIYTPSKSTTAKLLSGATWSISYGDGSSSSGDVYTDTVSVGGLTVTGQAVESAKKVSSSFTEDSTIDGLLGLAFSTLNTVSPTQQKTFFDNAKASLDSPVFTADLGYHAPGTYNFGFIDTTAYTGSITYTAVSTKQGFWEWTSTGYAVGSGTFKSTSIDGIADTGTTLLYLPATVVSAYWAQVSGAKSSSSVGGYVFPCSATLPSFTFGVGSARIVIPGDYIDFGPISTGSSSCFGGIQSSAGIGINIFGDVALKAAFVVFNGATTPTLGFASK 419
               SCOP domains d1gvxa_ A: Endothiapepsin                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ----1gvxA01 A:5-174 Acid Proteases                                                                                                                                            1gvxA02 A:175-329 Acid Proteases                                                                                                                           - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ................eeeeeee....eeeeeeee.....eee.....hhhhh.-....hhhhh...eeeeeeeeeee.....eeeeeeeeeeeee..eeeeeeeeeeeeeehhhhhhh....eeee..hhhhh........hhhhhhh..............................................eeeeeeeee.....eeeeeeeee......eeehhhhhhhhhh.....eee....eeeee.......eeeee..eeeeehhhh.eeee......eeee.eee......eeehhhhhh................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ----------------PEPTIDASE_A1  PDB: A:17-328 UniProt: 106-417                                                                                                                                                                                                                                                                            -- PROSITE (1)
                PROSITE (2) -------------------------------ASP_PROTEASE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1gvx A   1 STGSATTTPIDSLDDAYITPVQIGTPAQTLNLDFDTGSSDLWVFSSETTASEVd-QTIYTPSKSTTAKLLSGATWSISYGDGSSSSGDVYTDTVSVGGLTVTGQAVESAKKVSSSFTEDSTIDGLLGLAFSTLNTVSPTQQKTFFDNAKASLDSPVFTADLGYHAPGTYNFGFIDTTAYTGSITYTAVSTKQGFWEWTSTGYAVGSGTFKSTSIDGIADTGTTLLYLPATVVSAYWAQVSGAKSSSSVGGYVFPCSATLPSFTFGVGSARIVIPGDYIDFGPISTGSSSCFGGIQSSAGIGINIFGDVALKAAFVVFNGATTPTLGFASK 330
                                    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       330
                                                                                54-SUI                                                                                                                                                                                                                                                                                
                                                                                  56

Chain I from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 1gvx I 401 PTExRE 406
                               |  
                             404-PUK

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(

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Folds(

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Superfamilies( (-)

)

Families(

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Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Acid proteases (1120)

Superfamily: Acid proteases (1120)

Family: Pepsin-like (505)

Protein domain: Endothiapepsin (46)

Chestnut blight fungus (Endothia parasitica) [TaxId: 5116] (46)

d1gvxa_

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)

Chestnut blight fungus (Endothia parasitica) (5)

1a	1gvxA02	A:175-329
1b	1gvxA01	A:5-174

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CARP_CRYPA | P11838)

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/Biological Unit
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	Ligands, Modified Residues, Ions
		PUK	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Cis Peptide Bonds
		Ser A:137 - Pro A:138	[ RasMol ]
		Thr A:25 - Pro A:26	[ RasMol ]

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	1gvx
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	3.4.23.22
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		Disease Information	:	OMIM

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		Interatomic Contacts of Structural Units	:	CSU
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1e5o	ENDOTHIAPEPSIN COMPLEX WITH INHIBITOR DB2
1e80	ENDOTHIAPEPSIN COMPLEX WITH RENIN INHIBITOR MERCK-KGAA- EMD56133
1e81	ENDOTHIAPEPSIN COMPLEX WITH RENIN INHIBITOR MERCK-KGAA- EMD61395
1e82	ENDOTHIAPEPSIN COMPLEX WITH RENIN INHIBITOR MERCK-KGAA- EMD59601
1eed	ENDOTHIAPEPSIN COMPLEX WITH THE CYCLOHEXYL RENIN INHIBITOR PD125754
1ent	ENDOTHIAPEPSIN COMPLEX WITH THE INHIBITOR PD130328
1epl
1epm
1epn
1epo
1epp
1epq
1epr
1er8
1gkt	NEUTRON LAUE DIFFRACTION STRUCTURE OF ENDOTHIAPEPSIN COMPLEXED WITH TRANSITION STATE ANALOGUE INHIBITOR H261
1gvt	ENDOTHIAPEPSIN COMPLEX WITH CP-80,794
1gvu	ENDOTHIAPEPSIN COMPLEX WITH H189
1gvv	FIVE ATOMIC RESOLUTION STRUCTURES OF ENDOTHIAPEPSIN INHIBITOR COMPLEXES; IMPLICATIONS FOR THE ASPARTIC PROTEINASE MECHANISM
1gvw	ENDOTHIAPEPSIN COMPLEX WITH PD-130,328
2er0
2er6
2er7
2er9
3er3
3er5
4ape
4er1
4er2
4er4
5er1
5er2

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (3, 3)

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

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SCOP Domains (1, 1)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (4, 4)

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