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Title :   CRYSTAL STRUCTURE OF ( (2S)-5-AMINO-2-((1-N-PROPYL-1H-IMIDAZOL-4-YL)METHYL)PENTANOIC ACID) UK396,082 A TAFIA INHIBITOR, BOUND TO ACTIVATED PORCINE PANCREATIC CARBOXYPEPTIDASEB

Authors :   D. G. Brown, R. S. Moore

Date :   24 Jan 07 (Deposition) - 20 Nov 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

Chains :   Asym./Biol. Unit : A

Keywords :   3D-Structure, Carboxypeptidase, Carboxypeptidase B, Direct Metal-Binding, Metalloprotease, Protease, Hydrolase, Zinc, Zymogen, Exopeptidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. E. Bunnage, J. Blagg, J. Steele, D. R. Owen, C. Allerton, A. B. Mcelroy, D. Miller, T. Ringer, K. Butcher, K. Beaumont, K. Evans, A. J. Gray, S. J. Holland, N. Feeder, R. S. Moore, D. G. Brown
Discovery Of Potent & Selective Inhibitors Of Activated Thrombin-Activatable Fibrinolysis Inhibitor For The Treatment Of Thrombosis.
J. Med. Chem. V. 50 6095 2007
PubMed-ID: 17990866 | Reference-DOI: 10.1021/JM0702433

Molecule 1 - CARBOXYPEPTIDASE B
	Chains	:	A
	EC Number	:	3.4.17.2
	Fragment	:	CATALYTIC DOMAIN, RESIDUES 111-416
	Organism Common	:	PIG
	Organism Scientific	:	SUS SCROFA
	Organism Taxid	:	9823
	Other Details	:	PURCHASED
	Synonym	:	ACTIVATED PORCINE PANCREATIC CARBOXYPEPTIDASE B
	Tissue	:	PANCREATIC

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	720	1	Ligand/Ion	(2S)-5-AMINO-2-[(1-PROPYL-1H-IMIDAZOL-4-YL)METHYL]PENTANOIC ACID
2	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:85 , ASP A:159 , ASP A:162 , GLU A:291 , HOH A:2302	BINDING SITE FOR RESIDUE ZN A1308
2	AC2	SOFTWARE	HIS A:69 , GLU A:72 , HIS A:196 , 720 A:1310	BINDING SITE FOR RESIDUE ZN A1309
3	AC3	SOFTWARE	HIS A:69 , GLU A:72 , ASN A:144 , ARG A:145 , HIS A:196 , SER A:197 , TYR A:198 , SER A:207 , ASP A:255 , GLU A:270 , ZN A:1309 , HOH A:2257 , HOH A:2271 , HOH A:2303 , HOH A:2304	BINDING SITE FOR RESIDUE 720 A1310

Asymmetric/Biological Unit

No.	Residues
1	A:66	-	A:79
2	A:138	-	A:161

(no "Cis Peptide Bond" information available for 2JEW)

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

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CARBOXYPEPT_ZN_1	PS00132	Zinc carboxypeptidases, zinc-binding region 1 signature.	CBPB1_PIG	167-189	1	A:60-82
2	CARBOXYPEPT_ZN_2	PS00133	Zinc carboxypeptidases, zinc-binding region 2 signature.	CBPB1_PIG	304-314	1	A:196-206

(no "Exon" information available for 2JEW)

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:304
 aligned with CBPB1_PIG | P09955 from UniProtKB/Swiss-Prot  Length:416

    Alignment length:304
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412    
           CBPB1_PIG    113 GHSYEKYNNWETIEAWTKQVTSENPDLISRTAIGTTFLGNNIYLLKVGKPGPNKPAIFMDCGFHAREWISHAFCQWFVREAVLTYGYESHMTEFLNKLDFYVLPVLNIDGYIYTWTKNRMWRKTRSTNAGTTCIGTDPNRNFDAGWCTTGASTDPCDETYCGSAAESEKETKALADFIRNNLSSIKAYLTIHSYSQMILYPYSYDYKLPENNAELNNLAKAAVKELATLYGTKYTYGPGATTIYPAAGGSDDWAYDQGIKYSFTFELRDKGRYGFILPESQIQATCEETMLAIKYVTNYVLGHL  416
               SCOP domains d2jewa_ A: automated matches                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeee........eeeee......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhheeeee...hhhhhhhhhhh...................hhhhh..........................hhhhhhhhhhhhhh...eeeeeeeee...eeee..........hhhhhhhhhhhhhhhhhh......eeeehhhhh.....hhhhhhhhh...eeeeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------CARBOXYPEPT_ZN_1       ------------------------------------------------------------------------------------------------------------------CARBOXYPEPT------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2jew A    6 GHSYEKYNNWETIEAWTKQVTSENPDLISRTAIGTTFLGNNIYLLKVGKPGPNKPAIFMDCGFHAREWISHAFCQWFVREAVLTYGYESHMTEFLNKLDFYVLPVLNIDGYIYTWTKNRMWRKTRSTNAGTTCIGTDPNRNFDAGWCTTGASTDPCDETYCGSAAESEKETKALADFIRNNLSSIKAYLTIHSYSQMILYPYSYDYKLPENNAELNNLAKAAVKELATLYGTKYTYGPGATTIYPAAGGSDDWAYDQGIKYSFTFELRDKGRYGFILPESQIQATCEETMLAIKYVTNYVLGHL  308
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185  |    194       204       214       224       234       244       254       264       274       284       294       304    
                                                                                                                                                                                                               187A

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Phosphorylase/hydrolase-like (558)

Superfamily: Zn-dependent exopeptidases (214)

Family: Pancreatic carboxypeptidases (77)

Protein domain: automated matches (23)

Pig (Sus scrofa) [TaxId: 9823] (21)

d2jewa_

(no "CATH Domain" information available for 2JEW)

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CBPB1_PIG | P09955)

molecular function
	GO:0004180	carboxypeptidase activity	Catalysis of the hydrolysis of the terminal or penultimate peptide bond at the C-terminal end of a peptide or polypeptide.
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004181	metallocarboxypeptidase activity	Catalysis of the hydrolysis of C-terminal amino acid residues from a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	GO:0008237	metallopeptidase activity	Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	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.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
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.
	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/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2jew)

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	2jew
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	3.4.17.2
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1nsa	THREE-DIMENSIONAL STRUCTURE OF PORCINE PROCARBOXYPEPTIDASE B: A STRUCTURAL BASIS OF ITS INACTIVITY
1pba	PROCARBOXYPEPTIDASE B (ACTIVATION DOMAIN) (NMR , 19 STRUCTURES)
1z5r	CRYSTAL STRUCTURE OF ACTIVATED PORCINE PANCREATICCARBOXYPEPTIDASE B
1zg7	CRYSTAL STRUCTURE OF 2-(5-{[AMINO(IMINO) METHYL]AMINO}-2-CHLOROPHENYL)-3- SULFANYLPROPANOIC ACID BOUND TO ACTIVATEDPORCINE PANCREATIC CARBOXYPEPTIDASE B
1zg8	CRYSTAL STRUCTURE OF (R)-2-(3-{[AMINO( IMINO)METHYL]AMINO}PHENYL)-3-SULFANYLPROPANOIC ACID BOUND TOACTIVATED PORCINE PANCREATIC CARBOXYPEPTIDASE B
1zg9	CRYSTAL STRUCTURE OF 5-{[AMINO(IMINO)METHYL ]AMINO}-2-(SULFANYLMETHYL)PENTANOIC ACID BOUND TO ACTIVATED PORCINEPANCREATIC CARBOXYPEPTIDASE B

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

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