2ZCL - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF HUMAN PROSTATE SPECIFIC ANTIGEN COMPLEXED WITH AN ACTIVATING ANTIBODY

Authors :   R. Menez, E. Stura, C. Jolivet-Reynaud

Date :   09 Nov 07 (Deposition) - 29 Jan 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.25

Chains :   Asym./Biol. Unit : H,L,P

Keywords :   Human Psa, Antibodies, Kallikrein Related Peptidases, Prostate Cancer, Glycoprotein, Hydrolase, Protease, Secreted, Serine Protease, Zymogen, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Michel, B. H. Muller, M. Bossus, F. Ducancel, C. Jolivet-Reynaud, E. A. Stura
Crystal Structure Of A Ternary Complex Between Human Prostate-Specific Antigen, Its Substrate Acyl Intermediate And An Activating Antibody
J. Mol. Biol. V. 376 1021 2008
PubMed-ID: 18187150 | Reference-DOI: 10.1016/J.JMB.2007.11.052

Molecule 1 - PROSTATE-SPECIFIC ANTIGEN
	Chains	:	P
	EC Number	:	3.4.21.77
	Fragment	:	UNP RESIDUES 25-261
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	HUMAN SEMINAL FLUIDS
	Synonym	:	PSA, KALLIKREIN- 3, SEMENOGELASE, GAMMA-SEMINOPROTEIN, SEMININ, P-30 ANTIGEN

Molecule 2 - MONOCLONAL ANTIBODY 8G8F5 FAB
	Chains	:	L
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	ASCITIC FLUIDS
	Strain	:	BALB/CJYCO

Molecule 3 - MONOCLONAL ANTIBODY 8G8F5 FAB
	Chains	:	H
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	ASCITIC FLUIDS
	Strain	:	BALB/CJYCO

		1	2	3
Asymmetric/Biological Unit	:	H	L	P

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG P:60 , ASN P:61 , NAG P:403	BINDING SITE FOR RESIDUE NAG P 401
2	AC2	SOFTWARE	NAG P:401	BINDING SITE FOR RESIDUE NAG P 403

Asymmetric/Biological Unit

No.	Residues
1	H:22	-	H:92
2	H:140	-	H:195
3	L:23	-	L:88
4	L:134	-	L:194
5	P:22	-	P:157
6	P:42	-	P:58
7	P:136	-	P:201
8	P:168	-	P:182
9	P:191	-	P:220

Asymmetric/Biological Unit

No.	Residues
1	Glu P:218	-	Pro P:219
2	Ser L:7	-	Pro L:8
3	Gln L:76	-	Pro L:77
4	Asp L:94	-	Pro L:95
5	Tyr L:140	-	Pro L:141
6	Phe H:146	-	Pro H:147
7	Trp H:188	-	Pro H:189

Asymmetric/Biological Unit (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_021941	E	32	K	KLK3_HUMAN	Polymorphism	2271092	P	E	23	K
2	UniProt	VAR_021942	L	132	I	KLK3_HUMAN	Polymorphism	2003783	P	L	114	I
3	UniProt	VAR_051852	I	179	T	KLK3_HUMAN	Polymorphism	17632542	P	I	163	T

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

Asymmetric/Biological Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	KLK3_HUMAN	25-258	1	P:16-243
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	KLK3_HUMAN	61-66	1	P:53-58
3	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	KLK3_HUMAN	207-218	1	P:189-200

Asymmetric/Biological Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000326003	1	ENSE00001123926	chr19:51358171-51358257	87	KLK3_HUMAN	1-16	16	0	-	-
1.2a	ENST00000326003	2a	ENSE00001718125	chr19:51359496-51359655	160	KLK3_HUMAN	16-69	54	1	P:16-61 (gaps)	46
1.3b	ENST00000326003	3b	ENSE00001268279	chr19:51361285-51361571	287	KLK3_HUMAN	69-165	97	1	P:61-149 (gaps)	100
1.4	ENST00000326003	4	ENSE00001268316	chr19:51361715-51361851	137	KLK3_HUMAN	165-210	46	1	P:149-192	46
1.5b	ENST00000326003	5b	ENSE00001268296	chr19:51363228-51364020	793	KLK3_HUMAN	211-261	51	1	P:193-246 (gaps)	55

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 H from PDB  Type:PROTEIN  Length:230
                                                                                                                                                                                                                                                                       
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2zclH01 H:1-113 Immunoglobulins                                                                                           2zclH02 H:114-212 Immunoglobulins                                                                  --------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh...eeeeehhh.eeeeee...hhhhheeeeeee............ee....eeee.........eeee...........eeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeee..........eeeeee....eeeeee............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2zcl H    1 QVQLQQSGDDLVKPGASVKLSCKASGYTFTTYYINWMRQRPGQGLEWIGRIAPASGTTYSSEMFKDKATLTVDTSSNTAYIQLSSLSSEDSAVYFCARADYGFNSGEAMDYWGQGTSVTVSSAKTTAPPVYPLAPVCGDTTGSSVTLGCLVKGYFPESVTLLWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIVPRDCGCKPCI  221
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||101       111       121       131       141       151       161       171       181       191       201       211       221
                                                                              52A                            82A||               100A||||                                                                                                                         
                                                                                                              82B|                100B|||                                                                                                                         
                                                                                                               82C                 100C||                                                                                                                         
                                                                                                                                    100D|                                                                                                                         
                                                                                                                                     100E

Chain L from PDB  Type:PROTEIN  Length:218
 aligned with KV3AD_MOUSE | P01665 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:218
                                                                                                                                        111                                                                                                           
                                    10        20        30        40        50        60        70        80        90       100       110|        -         -         -         -         -         -         -         -         -         -        
         KV3AD_MOUSE      1 DIVLTQSPASLAVSLGQRATISCKASQSVDYDGDSYMNWYQQKPGQPPKLLIYAASNLESGIPARFSGSGSGTDFTLNIHPVEEEDAATYYCQQSNEDPFTFGSGTKLEIK-----------------------------------------------------------------------------------------------------------    -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2zclL01 L:1-108 Immunoglobulins                                                                                 2zclL02 L:109-214 Immunoglobulins                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee....ee..ee.eeeeee.....eeeee.............eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee....eeeeeee..eee...ee............eeeeeeeeeehhhhh...eeeeeeee..eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2zcl L    1 DIVLTQSPASLAVSLGQRATISCKASQSVDFDGDSYMNWYQQKPGQPPKLLIFAASNLASGIPARLSGSGSGTDFTLNIQPVEEEDAATYYCQQSNEDPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  214
                                    10        20       27C|       36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206        
                                                     27A|||                                                                                                                                                                                           
                                                      27B||                                                                                                                                                                                           
                                                       27C|                                                                                                                                                                                           
                                                        27D

Chain P from PDB  Type:PROTEIN  Length:237
 aligned with KLK3_HUMAN | P07288 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:237
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       
          KLK3_HUMAN     25 IVGGWECEKHSQPWQVLVASRGRAVCGGVLVHPQWVLTAAHCIRNKSVILLGRHSLFHPEDTGQVFQVSHSFPHPLYDMSLLKNRFLRPGDDSSHDLMLLRLSEPAELTDAVKVMDLPTQEPALGTTCYASGWGSIEPEEFLTPKKLQCVDLHVISNDVCAQVHPQKVTKFMLCAGRWTGGKSTCSGDSGGPLVCNGVLQGITSWGSEPCALPERPSLYTKVVHYRKWIKDTIVANP  261
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2zclP01     2zclP02 P:28-120,P:233-245 Trypsin-like serine proteases                                              2zclP01 P:16-27,P:121-232 Trypsin-like serine proteases                                                      2zclP02      - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeee....eeeeeeeee..eeeehhhhh....eeee............eeeeeeeeee....hhhhhhh.............eeeee........................eeeeee...............eeeeeee.hhhhhhhhh.......eeeee...............eeee..eeeeeeee...........eeeee...hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------K---------------------------------------------------------------------------------------------------I----------------------------------------------T---------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: P:16-243 UniProt: 25-258                                                                                                                                                                                                --- PROSITE (1)
                PROSITE (2) ------------------------------------TRYPSI--------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2a  PDB: P:16-61 (gaps) UniProt: 16-69-----------------------------------------------------------------------------------------------Exon 1.4  PDB: P:149-192 UniProt: 165-210     Exon 1.5b  PDB: P:193-246 (gaps) UniProt: 211-261   Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------Exon 1.3b  PDB: P:61-149 (gaps) UniProt: 69-165                                                  ------------------------------------------------------------------------------------------------ Transcript 1 (2)
                2zcl P   16 IVGGWECEKHSQPWQVLVASRGRAVCGGVLVHPQWVLTAAHCIRNKSVILLGRHSLFHPEDTGQVFQVSHSFPHPLYDMSLLKNRFLRPGDDSSHDLMLLRLSEPAELTDAVKVMDLPTQEPALGTTCYASGWGSIEPEEFLTPKKLQCVDLHVISNDVCAQVHPQKVTKFMLCAGRWTGGKSTCSGDSGGPLVCNGVLQGITSWGSEPCALPERPSLYTKVVHYRKWIKDTIVANP  246
                                    25        35   ||   46        56        66      ||77        87       95B||||||||96       106       116       128       138       148       158       168       178      186B       196      |210       220   |   229       239       
                                                  39|                              73|                  95A||||||95J|                           125|                                                       186A|              203|            223A                       
                                                   41                               75                   95B||||||95K                            128                                                        186B               208                                       
                                                                                                          95C||||||                                                                                                                                                      
                                                                                                           95D|||||                                                                                                                                                      
                                                                                                            95E||||                                                                                                                                                      
                                                                                                             95F|||                                                                                                                                                      
                                                                                                              95G||                                                                                                                                                      
                                                                                                               95H|                                                                                                                                                      
                                                                                                                95I

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 "SCOP Domain" information available for 2ZCL)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Thrombin, subunit H (1535)

Homologous Superfamily: Trypsin-like serine proteases (1488)

Human (Homo sapiens) (615)

1a	2zclP02	P:28-120,P:233-245
1b	2zclP01	P:16-27,P:121-232

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Human (Homo sapiens) (912)

2a	2zclL02	L:109-214
2b	2zclL01	L:1-108
2c	2zclH02	H:114-212
2d	2zclH01	H:1-113

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain L (KV3AD_MOUSE | P01665)

molecular function
	GO:0003823		antigen binding		Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.

Chain P (KLK3_HUMAN | P07288)

molecular function
	GO:0004175	endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
	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:0016811	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides	Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a linear amide.
	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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0008236	serine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
	GO:0002778	antibacterial peptide production	The synthesis or release of an antibacterial peptide during an immune response, resulting in an increase in intracellular or extracellular levels.
	GO:0044267	cellular protein metabolic process	The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
	GO:0016525	negative regulation of angiogenesis	Any process that stops, prevents, or reduces the frequency, rate or extent of angiogenesis.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	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.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0043234	protein complex	A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Asp L:94 - Pro L:95	[ RasMol ]
		Gln L:76 - Pro L:77	[ RasMol ]
		Glu P:218 - Pro P:219	[ RasMol ]
		Phe H:146 - Pro H:147	[ RasMol ]
		Ser L:7 - Pro L:8	[ RasMol ]
		Trp H:188 - Pro H:189	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]

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	2zcl
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2zch	CRYSTAL STRUCTURE OF HUMAN PSA COMPLEXED WITH ANTIBODY 8G8F5 AT PH7.2
2zck	CRYSTAL STRUCTURE OF HUMAN PSA AND ITS SUBSTRATE-ACYL INTERMEDIATE COMPLEXED WITH ANTIBODY 8G8F5 AT PH7.3

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (9, 9)

Cis Peptide Bonds (7, 7)

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SAPs(SNPs)/Variants (3, 3)

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Exons (4, 4)

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SCOP Domains (0, 0)

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