1ZLI - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF THE TICK CARBOXYPEPTIDASE INHIBITOR IN COMPLEX WITH HUMAN CARBOXYPEPTIDASE B

Authors :   J. L. Arolas, G. M. Popowicz, J. Lorenzo, C. P. Sommerhoff, R. Huber, F. X. Aviles, T. A. Holak

Date :   06 May 05 (Deposition) - 05 Jul 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.09

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

Keywords :   Inhibitor-Metallocarboxypeptidase Complex, Beta-Defensin Fold (Tci), Eight-Stranded Twisted Beta-Sheet Surrounded By Eight Alpha-Helices (Cpb), Hydrolase/Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. L. Arolas, G. M. Popowicz, J. Lorenzo, C. P. Sommerhoff, R. Huber, F. X. Aviles, T. A. Holak
The Three-Dimensional Structures Of Tick Carboxypeptidase Inhibitor In Complex With A/B Carboxypeptidases Reveal A Novel Double-Headed Binding Mode
J. Mol. Biol. V. 350 489 2005
PubMed-ID: 15961103 | Reference-DOI: 10.1016/J.JMB.2005.05.015
(for further references see the PDB file header)

Molecule 1 - CARBOXYPEPTIDASE B
	Chains	:	A
	EC Number	:	3.4.17.2
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Plasmid	:	PPIC9
	Expression System Strain	:	KM71
	Expression System Taxid	:	4922
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CPB, METALLOCARBOXYPEPTIDASE, PANCREAS-SPECIFIC PROTEIN, PASP

Molecule 2 - CARBOXYPEPTIDASE INHIBITOR
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PBAT4
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	RHIPICEPHALUS BURSA
	Organism Taxid	:	67831
	Synonym	:	INHIBITOR OF A/B METALLOCARBOXYPEPTIDASES

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	ZN	1	Ligand/Ion	ZINC ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:69 , GLU A:72 , HIS A:196 , LEU B:74	BINDING SITE FOR RESIDUE ZN A 501

Asymmetric/Biological Unit

No.	Residues
1	A:66	-	A:79
2	A:138	-	A:161
3	A:152	-	A:166
4	B:3	-	B:31
5	B:10	-	B:27
6	B:16	-	B:32
7	B:40	-	B:70
8	B:47	-	B:64
9	B:54	-	B:71

Asymmetric/Biological Unit

No.	Residues
1	Ser A:197	-	Tyr A:198
2	Pro A:205	-	Tyr A:206
3	Arg A:272	-	Asp A:273

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_048598	D	208	N	CBPB1_HUMAN	Polymorphism	1059502	A	N	101	N

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

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_HUMAN	167-189	1	A:60-82
2	CARBOXYPEPT_ZN_2	PS00133	Zinc carboxypeptidases, zinc-binding region 2 signature.	CBPB1_HUMAN	304-314	1	A:196-206

Asymmetric/Biological Unit (8, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.4a	ENST00000282957	4a	ENSE00001008267	chr3:148545441-148545681	241	CBPB1_HUMAN	1-24	24	0	-	-
1.5b	ENST00000282957	5b	ENSE00001008280	chr3:148545789-148545864	76	CBPB1_HUMAN	24-49	26	0	-	-
1.6b	ENST00000282957	6b	ENSE00001008270	chr3:148552285-148552409	125	CBPB1_HUMAN	50-91	42	0	-	-
1.8c	ENST00000282957	8c	ENSE00001008276	chr3:148558473-148558572	100	CBPB1_HUMAN	91-124	34	1	A:5-17	13
1.8e	ENST00000282957	8e	ENSE00001008269	chr3:148558661-148558762	102	CBPB1_HUMAN	125-158	34	1	A:18-51	34
1.9b	ENST00000282957	9b	ENSE00001008275	chr3:148559610-148559711	102	CBPB1_HUMAN	159-192	34	1	A:52-85	34
1.10b	ENST00000282957	10b	ENSE00001008268	chr3:148562265-148562375	111	CBPB1_HUMAN	193-229	37	1	A:86-122	37
1.11c	ENST00000282957	11c	ENSE00001008272	chr3:148562464-148562554	91	CBPB1_HUMAN	230-260	31	1	A:123-153	31
1.12	ENST00000282957	12	ENSE00001008274	chr3:148563211-148563413	203	CBPB1_HUMAN	260-327	68	1	A:153-219 (gaps)	70
1.13c	ENST00000282957	13c	ENSE00001077919	chr3:148575244-148575328	85	CBPB1_HUMAN	328-356	29	1	A:220-248	29
1.14a	ENST00000282957	14a	ENSE00001077921	chr3:148577602-148577943	342	CBPB1_HUMAN	356-417	62	1	A:248-309	62

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:306
 aligned with CBPB1_HUMAN | P15086 from UniProtKB/Swiss-Prot  Length:417

    Alignment length:306
                                   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_HUMAN    112 TGHSYEKYNKWETIEAWTQQVATENPALISRSVIGTTFEGRAIYLLKVGKAGQNKPAIFMDCGFHAREWISPAFCQWFVREAVRTYGREIQVTELLDKLDFYVLPVLNIDGYIYTWTKSRFWRKTRSTHTGSSCIGTDPNRNFDAGWCEIGASRNPCDETYCGPAAESEKETKALADFIRNKLSSIKAYLTIHSYSQMMIYPYSYAYKLGENNAELNALAKATVKELASLHGTKYTYGPGATTIYPAAGGSDDWAYDQGIRYSFTFELRDTGRYGFLLPESQIRATCEETFLAIKYVASYVLEHLY  417
               SCOP domains d1zlia1 A:5-309 Carboxypeptidase B                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeee........eeeee.......hhhhhhhhhhhhhhhhhh..hhhhhhhhhhheeeee...hhhhhhhhhhh...................hhhhh..........................hhhhhhhhhhhhhh...eeeeeeee....eeee..........hhhhhhhhhhhhhhhhhh......eeeehhhhh.....hhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------N----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------CARBOXYPEPT_ZN_1       ------------------------------------------------------------------------------------------------------------------CARBOXYPEPT------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.8c    Exon 1.8e  PDB: A:18-51           Exon 1.9b  PDB: A:52-85           Exon 1.10b  PDB: A:86-122            Exon 1.11c  PDB: A:123-153     -------------------------------------------------------------------Exon 1.13c  PDB: A:220-248   ------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.12  PDB: A:153-219 (gaps) UniProt: 260-327                   ----------------------------Exon 1.14a  PDB: A:248-309 UniProt: 356-417                    Transcript 1 (2)
                1zli A    5 TGHSYEKYNNWETIEAWTQQVATENPALISRSVIGTTFEGRAIYLLKVGKAGQNKPAIFMDCGFHAREWISPAFCQWFVREAVRTYGREIQVTELLNKLDFYVLPVLNIDGYIYTWTKSRFWRKTRSTHTGSSCIGTDPNRNFDAGWCEIGASRNPCDETYCGPAAESEKETKALADFIRNKLSSIKAYLTIHSYSQMMIYPYSYAYKLGENNAELNALAKATVKELASLHGTKYTYGPGATTIYPAAGGSDDWAYDQGIRYSFTFELRDTGRYGFLLPESQIRATCEETFLAIKYVASYVLEHLY  309
                                    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      
                                                                                                                                                                                                                 188||                                                                                                                        
                                                                                                                                                                                                                 1889|                                                                                                                        
                                                                                                                                                                                                                   189

Chain B from PDB  Type:PROTEIN  Length:74
 aligned with TCI1_RHIBU | Q5EPH2 from UniProtKB/Swiss-Prot  Length:97

    Alignment length:74
                                    32        42        52        62        72        82        92    
          TCI1_RHIBU     23 NECVSKGFGCLPQSDCPQEARLSYGGCSTVCCDLSKLTGCKGKGGECNPLDRQCKELQAESASCGKGQKCCVWL   96
               SCOP domains d1zlib1 B:1-37                       d1zlib2 B:38-74                       SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh..eeehhhhhhhhhh........eeehhhhh..hhhhh.eeee.......hhhhhhhhh..eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                1zli B    1 NECVSKGFGCLPQSDCPQEARLSYGGCSTVCCDLSKLTGCKGKGGECNPLDRQCKELQAESASCGKGQKCCVWL   74
                                    10        20        30        40        50        60        70

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 '\|'

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CBPB1_HUMAN | P15086)

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.

Chain B (TCI1_RHIBU | Q5EPH2)

molecular function
	GO:0004857	enzyme inhibitor activity	Binds to and stops, prevents or reduces the activity of an enzyme.
	GO:0008191	metalloendopeptidase inhibitor activity	Stops, prevents or reduces the activity of metalloendopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain and contain a chelated metal ion at their active sites which is essential to their catalytic activity.
	GO:0030414	peptidase inhibitor activity	Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
biological process
	GO:0044002	acquisition of nutrients from host	The process that begins with the production and formation of structures and molecules in an organism that are required for the acquisition and utilization of nutrients from its host organism, and the ends with the acquirement of the nutrients. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0007596	blood coagulation	The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
	GO:0042730	fibrinolysis	A process that solubilizes fibrin in the bloodstream of a multicellular organism, chiefly by the proteolytic action of plasmin.
	GO:0007599	hemostasis	The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
	GO:0010951	negative regulation of endopeptidase activity	Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
	GO:0010466	negative regulation of peptidase activity	Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
cellular component
	GO:0005575	cellular_component	The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
	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.

Asymmetric/Biological 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
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Arg A:272 - Asp A:273	[ RasMol ]
		Pro A:205 - Tyr A:206	[ RasMol ]
		Ser A:197 - Tyr A:198	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - 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
	1zli
		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
	CBPB1_HUMAN \| P15086
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	TCI1_RHIBU \| Q5EPH2
		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)
	3.4.17.2
		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
	CBPB1_HUMAN \| P15086
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	TCI1_RHIBU \| Q5EPH2
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	CBPB1_HUMAN \| P15086	:	1kwm
	TCI1_RHIBU \| Q5EPH2	:	1zlh 2jto 2k2x 2k2y 2k2z 3d4u 3lms 3osl

1zlh	CRYSTAL STRUCTURE OF THE TICK CARBOXYPEPTIDASE INHIBITOR IN COMPLEX WITH BOVINE CARBOXYPEPTIDASE A

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (9, 9)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (2, 2)

Exons (8, 8)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 3)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (20, 21)

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