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Title :   NEUTRON DIFFRACTION STRUCTURE OF ENDOTHIAPEPSIN IN COMPLEX WITH A GEM-DIOL INHIBITOR.

Authors :   L. Coates, H. -F. Tuan, S. Tomanicek, A. Kovalevsky, M. Mustyakimov, P. J. Cooper

Date :   17 Apr 08 (Deposition) - 27 May 08 (Release) - 12 Jul 17 (Revision)

Method :   NEUTRON DIFFRACTION

Resolution :   2.00

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

Keywords :   Acid Proteinase, Aspartyl Protease, Zymogen, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Coates, H. -F. Tuan, S. Tomanicek, A. Kovalevsky, M. Mustyakimov, P. Erskine, J. Cooper
The Catalytic Mechanism Of An Aspartic Proteinase Explored With Neutron And X-Ray Diffraction
J. Am. Chem. Soc. V. 130 7235 2008
PubMed-ID: 18479128 | Reference-DOI: 10.1021/JA801269X
(for further references see the PDB file header)

Molecule 1 - ENDOTHIAPEPSIN
	Chains	:	A
	EC Number	:	3.4.23.22
	Organism Common	:	CHESTNUT BLIGHT FUNGUS
	Organism Scientific	:	CRYPHONECTRIA PARASITICA
	Organism Taxid	:	5116
	Other Details	:	SUCCINAMIDE IS FORMED BETWEEN CHAIN A RESIDUES 54 AND 55.SIMILAR TO PDB 1GKT.
	Other Details - Source	:	ENDOTHIA PARASITICA FORMULA WEIGHT 33814.2
	Synonym	:	ASPARTATE PROTEASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 222)

No.	Name	Count	Type	Full Name
1	0QS	1	Ligand/Ion	N~2~-[(2R)-2-BENZYL-3-(TERT-BUTYLSULFONYL)PROPANOYL]-N-{(1R)-1-(CYCLOHEXYLMETHYL)-3,3-DIFLUORO-2,2-DIHYDROXY-4-[(2-MORPHOLIN-4-YLETHYL)AMINO]-4-OXOBUTYL}-3-(1H-IMIDAZOL-3-IUM-4-YL)-L-ALANINAMIDE
2	DOD	220	Ligand/Ion
3	SUI	1	Mod. Amino Acid	(3-AMINO-2,5-DIOXO-1-PYRROLIDINYL)ACETIC ACID

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	0QS	1	Ligand/Ion	N~2~-[(2R)-2-BENZYL-3-(TERT-BUTYLSULFONYL)PROPANOYL]-N-{(1R)-1-(CYCLOHEXYLMETHYL)-3,3-DIFLUORO-2,2-DIHYDROXY-4-[(2-MORPHOLIN-4-YLETHYL)AMINO]-4-OXOBUTYL}-3-(1H-IMIDAZOL-3-IUM-4-YL)-L-ALANINAMIDE
2	DOD	-1	Ligand/Ion
3	SUI	1	Mod. Amino Acid	(3-AMINO-2,5-DIOXO-1-PYRROLIDINYL)ACETIC ACID

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:10 , ASP A:15 , ASP A:33 , ASP A:35 , GLY A:37 , SER A:38 , TYR A:79 , GLY A:80 , ASP A:81 , SER A:83 , PHE A:116 , ASP A:119 , LEU A:125 , LEU A:133 , ASP A:219 , GLY A:221 , THR A:222 , THR A:223 , LEU A:224 , ILE A:300 , ILE A:304	BINDING SITE FOR RESIDUE 0QS A 400

Asymmetric Unit

No.	Residues
1	A:255	-	A:290

Asymmetric Unit

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

(no "SAP(SNP)/Variant" information available for 2VS2)

Asymmetric 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

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.	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 2VS2)

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
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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 d2vs2a_ A: automated matches                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ----2vs2A01 A:5-174 Acid Proteases                                                                                                                                            2vs2A02 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..eeeeehhhhheeee......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
                 2vs2 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

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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All beta proteins (24004)

Fold: Acid proteases (1120)

Superfamily: Acid proteases (1120)

Family: Pepsin-like (505)

Protein domain: automated matches (64)

Cryphonectria parasitica [TaxId: 5116] (21)

d2vs2a_

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Cathepsin D, subunit A; domain 1 (745)

Homologous Superfamily: Acid Proteases (745)

Chestnut blight fungus (Cryphonectria parasitica) (20)

1a	2vs2A02	A:175-329
1b	2vs2A01	A:5-174

(no "Pfam Domain" information available for 2VS2)

Asymmetric 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 Unit
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	Ligands, Modified Residues, Ions
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	Sites
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	Cis Peptide Bonds
		Ser A:137 - Pro A:138	[ RasMol ]
		Thr A:25 - Pro A:26	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	2vs2
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	CARP_CRYPA \| P11838
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	3.4.23.22
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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
1gvx	ENDOTHIAPEPSIN COMPLEXED WITH H256
1od1	ENDOTHIAPEPSIN PD135,040 COMPLEX
1oew	ATOMIC RESOLUTION STRUCTURE OF NATIVE ENDOTHIAPEPSIN
1oex	ATOMIC RESOLUTION STRUCTURE OF ENDOTHIAPEPSIN IN COMPLEX WITH A HYDROXYETHYLENE TRANSITION STATE ANALOGUE INHIBITOR H261
2er0
2er6
2er7
2er9
2jji	ENDOTHIAPEPSIN IN COMPLEX WITH A GEM-DIOL INHIBITOR.
2jjj	ENDOTHIAPEPSIN IN COMPLEX WITH A GEM-DIOL INHIBITOR.
2v00	X-RAY CRYSTAL STRUCTURE OF ENDOTHIAPEPSIN COMPLEXED WITH COMPOUND 1
3er3
3er5
4ape
4er1
4er2
4er4
5er1
5er2

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 222)

Sites (1, 1)

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)

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Related Entries Specified in the PDB File