3KGQ - JenaLib

Title :   CARBOXYPEPTIDASE A LIGANDED TO AN ORGANIC SMALL-MOLECULE: CONFORMATIONAL CHANGES

Authors :   D. Fernandez, E. Boix, I. Pallares, F. X. Aviles, J. Vendrell

Date :   29 Oct 09 (Deposition) - 27 Oct 10 (Release) - 12 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym./Biol. Unit : A

Keywords :   Intestinal Protease, Zinc-Metallocarboxypeptidase-Citrate Ternary Complex, Carboxypeptidase, Hydrolase, Metal-Binding, Metalloprotease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Fernandez, E. Boix, I. Pallares, F. X. Aviles, J. Vendrell
Structural And Functional Analysis Of The Complex Between Citrate And The Zinc Peptidase Carboxypeptidase A
Enzyme Res V. 2011 28676 2011
PubMed-ID: 21804935 | Reference-DOI: 10.4061/2011/128676

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 13)

Sites (12, 12)

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:69 , GLU A:72 , HIS A:196 , CIT A:310	BINDING SITE FOR RESIDUE ZN A 401
02	AC2	SOFTWARE	LEU A:15 , HIS A:120	BINDING SITE FOR RESIDUE NA A 402
03	AC3	SOFTWARE	HIS A:69 , GLU A:72 , ARG A:127 , ASN A:144 , ARG A:145 , HIS A:196 , SER A:197 , TYR A:248 , ALA A:250 , GLU A:270 , ZN A:401 , HOH A:431 , HOH A:535	BINDING SITE FOR RESIDUE CIT A 310
04	AC4	SOFTWARE	GLN A:37 , ARG A:40	BINDING SITE FOR RESIDUE ACN A 311
05	AC5	SOFTWARE	ILE A:244 , THR A:245 , ILE A:247 , HOH A:414	BINDING SITE FOR RESIDUE FMT A 312
06	AC6	SOFTWARE	SER A:199 , GLN A:200 , LEU A:201 , SER A:237 , LYS A:239 , HOH A:502	BINDING SITE FOR RESIDUE FMT A 313
07	AC7	SOFTWARE	TYR A:206 , LEU A:280 , HOH A:474	BINDING SITE FOR RESIDUE FMT A 314
08	AC8	SOFTWARE	ASN A:8 , VAL A:183 , GLY A:187 , ASN A:188 , PHE A:189 , GLN A:261 , ILE A:263 , HOH A:514	BINDING SITE FOR RESIDUE GOL A 315
09	AC9	SOFTWARE	TYR A:9 , TRP A:81 , LYS A:85 , GLU A:88 , HOH A:518	BINDING SITE FOR RESIDUE GOL A 317
10	BC1	SOFTWARE	GLU A:43 , GOL A:319 , HOH A:326	BINDING SITE FOR RESIDUE GOL A 318
11	BC2	SOFTWARE	GLU A:43 , GOL A:318	BINDING SITE FOR RESIDUE GOL A 319
12	BC3	SOFTWARE	TYR A:12 , ARG A:124 , LEU A:280 , LEU A:281	BINDING SITE FOR RESIDUE GOL A 320

SS Bonds (1, 1)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 3)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

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:303
 aligned with CBPA1_BOVIN | P00730 from UniProtKB/Swiss-Prot  Length:419

    Alignment length:303
                                   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   
          CBPA1_BOVIN   113 STNTFNYATYHTLDEIYDFMDLLVAEHPQLVSKLQIGRSYEGRPIYVLKFSTGGSNRPAIWIDLGIHSREWITQATGVWFAKKFTEDYGQDPSFTAILDSMDIFLEIVTNPDGFAFTHSQNRLWRKTRSVTSSSLCVGVDANRNWDAGFGKAGASSSPCSETYHGKYANSEVEVKSIVDFVKDHGNFKAFLSIHSYSQLLLYPYGYTTQSIPDKTELNQVAKSAVEALKSLYGTSYKYGSIITTIYQASGGSIDWSYNQGIKYSFTFELRDTGRYGFLLPASQIIPTAQETWLGVLTIMEHTL 415
               SCOP domains d3kgqa_ A: Carboxypeptidase A                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------Peptidase_M14-3kgqA01 A:18-296                                                                                                                                                                                                                                                         --------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeee........eeeeee.....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhheeeee...hhhhhhhhhhh...................hhhhh..........................hhhhhhhhhhhhhhh.eeeeeeee....eeee..........hhhhhhhhhhhhhhhhhh......eeeehhhhh.....hhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V------------------------------------------------A----------------------------------------------------------------------------V SAPs(SNPs)
                    PROSITE ---------------------------------------------------------CARBOXYPEPT_ZN_1       -----------------------------------------------------------------------------------------------------------------CARBOXYPEPT--------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kgq A   3 STNTFNYATYHTLDEIYDFMDLLVAEHPQLVSKLQIGRSYEGRPIYVLKFSTGGSNRPAIWIDLGIHSREWITQATGVWFAKKFTEDYGQDPSFTAILDSMDIFLEIVTNPDGFAFTHSQNRLWRKTRSVTSSSLCVGVDANRNWDAGFGKAGASSSPCSETYHGKYANSEVEVKSIVDFVKDHGNFKAFLSIHSYSQLLLYPYGYTTQSIPDKTELNQVAKSAVEALKSLYGTSYKYGSIITTIYQASGGSIDWSYNQGIKYSFTFELRDTGRYGFLLPASQIIPTAQETWLGVLTIMEHTL 305
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CBPA1_BOVIN | P00730)

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.

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	Cis Peptide Bonds
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