1ZG9 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF 5-{[AMINO(IMINO)METHYL]AMINO}-2-(SULFANYLMETHYL)PENTANOIC ACID BOUND TO ACTIVATED PORCINE PANCREATIC CARBOXYPEPTIDASE B

Authors :   M. Adler, J. Bryant, B. Buckman, I. Islam, B. Larsen, S. Finster, L. Kent, K. May, R. Mohan, S. Yuan, M. Whitlow

Date :   20 Apr 05 (Deposition) - 12 Jul 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)

Keywords :   Carboxypeptidase B, Exopeptidase, Thiol Based Inhibitor, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Adler, J. Bryant, B. Buckman, I. Islam, B. Larsen, S. Finster, L. Kent, K. May, R. Mohan, S. Yuan, M. Whitlow
Crystal Structures Of Potent Thiol-Based Inhibitors Bound To Carboxypeptidase B.
Biochemistry V. 44 9339 2005
PubMed-ID: 15982000 | Reference-DOI: 10.1021/BI0501941
(for further references see the PDB file header)

Molecule 1 - PROCARBOXYPEPTIDASE B
	Chains	:	A, B, C
	EC Number	:	3.4.17.2
	Fragment	:	CATALYTIC DOMAIN
	Organism Common	:	PIG
	Organism Scientific	:	SUS SCROFA
	Organism Taxid	:	9823

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	L06	3	Ligand/Ion	5-{[AMINO(IMINO)METHYL]AMINO}-2-(SULFANYLMETHYL)PENTANOIC ACID
2	ZN	3	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	L06	1	Ligand/Ion	5-{[AMINO(IMINO)METHYL]AMINO}-2-(SULFANYLMETHYL)PENTANOIC ACID
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	L06	1	Ligand/Ion	5-{[AMINO(IMINO)METHYL]AMINO}-2-(SULFANYLMETHYL)PENTANOIC ACID
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	L06	1	Ligand/Ion	5-{[AMINO(IMINO)METHYL]AMINO}-2-(SULFANYLMETHYL)PENTANOIC ACID
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:69 , GLU A:72 , HIS A:196 , L06 A:401	BINDING SITE FOR RESIDUE ZN A 400
2	AC2	SOFTWARE	HIS B:69 , GLU B:72 , HIS B:196 , L06 B:501	BINDING SITE FOR RESIDUE ZN B 500
3	AC3	SOFTWARE	HIS C:69 , GLU C:72 , HIS C:196 , L06 C:601	BINDING SITE FOR RESIDUE ZN C 600
4	AC4	SOFTWARE	HIS A:69 , GLU A:72 , ARG A:127 , ASN A:144 , ARG A:145 , HIS A:196 , LEU A:203 , SER A:207 , TYR A:248 , ALA A:250 , GLY A:253 , ASP A:255 , THR A:268 , GLU A:270 , ZN A:400 , HOH A:1022 , HOH A:1056	BINDING SITE FOR RESIDUE L06 A 401
5	AC5	SOFTWARE	HIS B:69 , GLU B:72 , ARG B:127 , ASN B:144 , ARG B:145 , HIS B:196 , LEU B:203 , SER B:207 , TYR B:248 , GLY B:253 , ASP B:255 , THR B:268 , GLU B:270 , ZN B:500 , HOH B:1142 , HOH B:1412	BINDING SITE FOR RESIDUE L06 B 501
6	AC6	SOFTWARE	HIS C:69 , GLU C:72 , ARG C:127 , ASN C:144 , ARG C:145 , HIS C:196 , SER C:207 , ILE C:247 , TYR C:248 , ALA C:250 , GLY C:253 , ASP C:255 , GLU C:270 , ZN C:600 , HOH C:1414	BINDING SITE FOR RESIDUE L06 C 601

Asymmetric Unit

No.	Residues
1	A:66	-	A:79
2	A:138	-	A:161
3	A:152	-	A:166
4	B:66	-	B:79
5	B:138	-	B:161
6	B:152	-	B:166
7	C:66	-	C:79
8	C:138	-	C:161
9	C:152	-	C:166

Asymmetric Unit

No.	Residues
1	Ser A:197	-	Tyr A:198
2	Pro A:205	-	Tyr A:206
3	Arg A:272	-	Asp A:273
4	Ser B:197	-	Tyr B:198
5	Pro B:205	-	Tyr B:206
6	Arg B:272	-	Asp B:273
7	Ser C:197	-	Tyr C:198
8	Pro C:205	-	Tyr C:206
9	Arg C:272	-	Asp C:273

(no "SAP(SNP)/Variant" information available for 1ZG9)

Asymmetric Unit (2, 6)

	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	3	A:60-82 B:60-82 C:60-82
2	CARBOXYPEPT_ZN_2	PS00133	Zinc carboxypeptidases, zinc-binding region 2 signature.	CBPB1_PIG	304-314	3	A:196-206 B:196-206 C:196-206

Biological Unit 1 (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 - -

Biological Unit 2 (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	- B:60-82 -
2	CARBOXYPEPT_ZN_2	PS00133	Zinc carboxypeptidases, zinc-binding region 2 signature.	CBPB1_PIG	304-314	1	- B:196-206 -

Biological Unit 3 (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	- - C:60-82
2	CARBOXYPEPT_ZN_2	PS00133	Zinc carboxypeptidases, zinc-binding region 2 signature.	CBPB1_PIG	304-314	1	- - C:196-206

(no "Exon" information available for 1ZG9)

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:305
 aligned with CBPB1_PIG | P09955 from UniProtKB/Swiss-Prot  Length:416

    Alignment length:305
                                   121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411     
           CBPB1_PIG    112 TGHSYEKYNNWETIEAWTKQVTSENPDLISRTAIGTTFLGNNIYLLKVGKPGPNKPAIFMDCGFHAREWISHAFCQWFVREAVLTYGYESHMTEFLNKLDFYVLPVLNIDGYIYTWTKNRMWRKTRSTNAGTTCIGTDPNRNFDAGWCTTGASTDPCDETYCGSAAESEKETKALADFIRNNLSSIKAYLTIHSYSQMILYPYSYDYKLPENNAELNNLAKAAVKELATLYGTKYTYGPGATTIYPAAGGSDDWAYDQGIKYSFTFELRDKGRYGFILPESQIQATCEETMLAIKYVTNYVLGHL  416
               SCOP domains d1zg9a_ 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...eeeeeeee....eeee..........hhhhhhhhhhhhhhhhhh......eeeehhhhh.....hhhhhhhh....eeeeee...........hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------CARBOXYPEPT_ZN_1       ------------------------------------------------------------------------------------------------------------------CARBOXYPEPT------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1zg9 A    5 TGHSYEKYNNWETIEAWTKQVTSENPDLISRTAIGTTFLGNNIYLLKVGKPGPNKPAIFMDCGFHAREWISHAFCQWFVREAVLTYGYESHMTEFLNKLDFYVLPVLNIDGYIYTWTKNRMWRKTRSTNAGTTCIGTDPNRNFDAGWCTTGASTDPCDETYCGSAAESEKETKALADFIRNNLSSIKAYLTIHSYSQMILYPYSYDYKLPENNAELNNLAKAAVKELATLYGTKYTYGPGATTIYPAAGGSDDWAYDQGIKYSFTFELRDKGRYGFILPESQIQATCEETMLAIKYVTNYVLGHL  308
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184   |   193       203       213       223       233       243       253       263       273       283       293       303     
                                                                                                                                                                                                                187A

Chain B from PDB  Type:PROTEIN  Length:305
 aligned with CBPB1_PIG | P09955 from UniProtKB/Swiss-Prot  Length:416

    Alignment length:305
                                   121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411     
           CBPB1_PIG    112 TGHSYEKYNNWETIEAWTKQVTSENPDLISRTAIGTTFLGNNIYLLKVGKPGPNKPAIFMDCGFHAREWISHAFCQWFVREAVLTYGYESHMTEFLNKLDFYVLPVLNIDGYIYTWTKNRMWRKTRSTNAGTTCIGTDPNRNFDAGWCTTGASTDPCDETYCGSAAESEKETKALADFIRNNLSSIKAYLTIHSYSQMILYPYSYDYKLPENNAELNNLAKAAVKELATLYGTKYTYGPGATTIYPAAGGSDDWAYDQGIKYSFTFELRDKGRYGFILPESQIQATCEETMLAIKYVTNYVLGHL  416
               SCOP domains d1zg9b_ B: automated matches                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhh....eeeeeeee.....eeeeeee........eeeee......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhheeeee...hhhhhhhhhhh...................hhhhh..........................hhhhhhhhhhhhhh...eeeeeeee....eeee..........hhhhhhhhhhhhhhhhhh......eeeehhhhh.....hhhhhhhhh...eeeeee...........hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------CARBOXYPEPT_ZN_1       ------------------------------------------------------------------------------------------------------------------CARBOXYPEPT------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1zg9 B    5 TGHSYEKYNNWETIEAWTKQVTSENPDLISRTAIGTTFLGNNIYLLKVGKPGPNKPAIFMDCGFHAREWISHAFCQWFVREAVLTYGYESHMTEFLNKLDFYVLPVLNIDGYIYTWTKNRMWRKTRSTNAGTTCIGTDPNRNFDAGWCTTGASTDPCDETYCGSAAESEKETKALADFIRNNLSSIKAYLTIHSYSQMILYPYSYDYKLPENNAELNNLAKAAVKELATLYGTKYTYGPGATTIYPAAGGSDDWAYDQGIKYSFTFELRDKGRYGFILPESQIQATCEETMLAIKYVTNYVLGHL  308
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184   |   193       203       213       223       233       243       253       263       273       283       293       303     
                                                                                                                                                                                                                187A

Chain C from PDB  Type:PROTEIN  Length:304
 aligned with CBPB1_PIG | P09955 from UniProtKB/Swiss-Prot  Length:416

    Alignment length:304
                                   121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411    
           CBPB1_PIG    112 TGHSYEKYNNWETIEAWTKQVTSENPDLISRTAIGTTFLGNNIYLLKVGKPGPNKPAIFMDCGFHAREWISHAFCQWFVREAVLTYGYESHMTEFLNKLDFYVLPVLNIDGYIYTWTKNRMWRKTRSTNAGTTCIGTDPNRNFDAGWCTTGASTDPCDETYCGSAAESEKETKALADFIRNNLSSIKAYLTIHSYSQMILYPYSYDYKLPENNAELNNLAKAAVKELATLYGTKYTYGPGATTIYPAAGGSDDWAYDQGIKYSFTFELRDKGRYGFILPESQIQATCEETMLAIKYVTNYVLGH  415
               SCOP domains d1zg9c_ C: automated matches                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------Peptidase_M14-1zg9C01 C:18-296                                                                                                                                                                                                                                                          ----------- Pfam domains (1)
           Pfam domains (2) -------------Peptidase_M14-1zg9C02 C:18-296                                                                                                                                                                                                                                                          ----------- Pfam domains (2)
           Pfam domains (3) -------------Peptidase_M14-1zg9C03 C:18-296                                                                                                                                                                                                                                                          ----------- Pfam domains (3)
         Sec.struct. author .........hhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeee........eeeee......hhhhhhhhhhhhhhhhh....hhhhhhhhhhheeeee...hhhhhhhhhhh...................hhhhh..........................hhhhhhhhhhhhh....eeeeeeee....eeee..........hhhhhhhhhhhhhhhhhh......eeeehhhhh.....hhhhhhhh....eeeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------CARBOXYPEPT_ZN_1       ------------------------------------------------------------------------------------------------------------------CARBOXYPEPT----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1zg9 C    5 TGHSYEKYNNWETIEAWTKQVTSENPDLISRTAIGTTFLGNNIYLLKVGKPGPNKPAIFMDCGFHAREWISHAFCQWFVREAVLTYGYESHMTEFLNKLDFYVLPVLNIDGYIYTWTKNRMWRKTRSTNAGTTCIGTDPNRNFDAGWCTTGASTDPCDETYCGSAAESEKETKALADFIRNNLSSIKAYLTIHSYSQMILYPYSYDYKLPENNAELNNLAKAAVKELATLYGTKYTYGPGATTIYPAAGGSDDWAYDQGIKYSFTFELRDKGRYGFILPESQIQATCEETMLAIKYVTNYVLGH  307
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184   |   193       203       213       223       233       243       253       263       273       283       293       303    
                                                                                                                                                                                                                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 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)

1a	d1zg9a_	A:
1b	d1zg9b_	B:
1c	d1zg9c_	C:

(no "CATH Domain" information available for 1ZG9)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_MH (119)

Family: Peptidase_M14 (33)

Sus scrofa (Pig) (18)

1a	Peptidase_M14-1zg9C01	C:18-296
1b	Peptidase_M14-1zg9C02	C:18-296
1c	Peptidase_M14-1zg9C03	C:18-296

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (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 Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Arg A:272 - Asp A:273	[ RasMol ]
		Arg B:272 - Asp B:273	[ RasMol ]
		Arg C:272 - Asp C:273	[ RasMol ]
		Pro A:205 - Tyr A:206	[ RasMol ]
		Pro B:205 - Tyr B:206	[ RasMol ]
		Pro C:205 - Tyr C:206	[ RasMol ]
		Ser A:197 - Tyr A:198	[ RasMol ]
		Ser B:197 - Tyr B:198	[ RasMol ]
		Ser C:197 - Tyr C:198	[ RasMol ]

Biological Units
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Access by PDB/NDB ID
	1zg9
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	CBPB1_PIG \| P09955
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	3.4.17.2
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1kwm	PRO FORM OF HUMAN PANCREATIC CARBOXYPEPTIDASE B
1nsa	PRO FORM OF PORCINE PANCREATIC CARBOXYPEPTIDASE B
1z5r	ACTIVED PORCINE PANCREATIC CARBOXYPEPTIDASE B
1zg7	THIOL BASED INHIBITOR BOUND TO PORCINE PANCREATIC CARBOXYPEPTIDASE B
1zg8	THIOL BASED INHIBITOR BOUND TO PORCINE PANCREATIC CARBOXYPEPTIDASE B

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (9, 9)

Cis Peptide Bonds (9, 9)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 6)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 3)

CATH Domains (0, 0)

Pfam Domains (1, 3)

Gene Ontology (10, 10)

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