1ZEB - JenaLib

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   X-RAY STRUCTURE OF ALKALINE PHOSPHATASE FROM HUMAN PLACENTA IN COMPLEX WITH 5'-AMP

Authors :   P. Llinas, E. A. Stura, A. Menez, Z. Kiss, T. Stigbrand, J. L. Millan, M. H

Date :   18 Apr 05 (Deposition) - 28 Jun 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Alkaline Phosphatase, 5'-Amp, Phosphoserine, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Llinas, E. A. Stura, A. Menez, Z. Kiss, T. Stigbrand, J. L. Millan, M. H. Le Du
Structural Studies Of Human Placental Alkaline Phosphatase In Complex With Functional Ligands.
J. Mol. Biol. V. 350 441 2005
PubMed-ID: 15946677 | Reference-DOI: 10.1016/J.JMB.2005.04.068

Molecule 1 - ALKALINE PHOSPHATASE
	Chains	:	A
	EC Number	:	3.1.3.1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PLAP-1, REGAN ISOZYME
	Tissue	:	PLACENTA

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 7)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	MG	1	Ligand/Ion	MAGNESIUM ION
3	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	SEP	1	Mod. Amino Acid	PHOSPHOSERINE
5	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	SEP	2	Mod. Amino Acid	PHOSPHOSERINE
5	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:122 , LEU A:258 , ARG A:297 , ARG A:301 , HOH A:991 , HOH A:1223 , HOH A:1384 , HOH A:1389 , HOH A:1417 , HOH A:1481 , HOH A:1551	BINDING SITE FOR RESIDUE NAG A 801
2	AC2	SOFTWARE	TRP A:248 , ASN A:249 , GLU A:252 , HOH A:1056 , HOH A:1287 , HOH A:1291 , HOH A:1303 , HOH A:1403	BINDING SITE FOR RESIDUE NAG A 803
3	AC3	SOFTWARE	SEP A:92 , ASP A:316 , HIS A:320 , HIS A:432	BINDING SITE FOR RESIDUE ZN A 901
4	AC4	SOFTWARE	ASP A:42 , SEP A:92 , ASP A:316 , ASP A:357 , HIS A:358	BINDING SITE FOR RESIDUE ZN A 902
5	AC5	SOFTWARE	ASP A:42 , SER A:155 , GLU A:311 , HOH A:910 , HOH A:927 , HOH A:937	BINDING SITE FOR RESIDUE MG A 903
6	AC6	SOFTWARE	GLU A:216 , PHE A:269 , GLU A:270 , ASP A:285 , HOH A:995	BINDING SITE FOR RESIDUE CA A 904

Asymmetric Unit

No.	Residues
1	A:121	-	A:183
2	A:467	-	A:474

(no "Cis Peptide Bond" information available for 1ZEB)

Asymmetric Unit (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_017419	P	25	L	PPB1_HUMAN	Polymorphism	1130335	A	P	3	L
2	UniProt	VAR_050520	I	89	L	PPB1_HUMAN	Polymorphism	13026692	A	I	67	L
3	UniProt	VAR_050521	R	231	P	PPB1_HUMAN	Polymorphism	1048988	A	R	209	P
4	UniProt	VAR_050522	R	263	H	PPB1_HUMAN	Polymorphism	2853378	A	R	241	H
5	UniProt	VAR_050523	E	451	G	PPB1_HUMAN	Polymorphism	1048994	A	E	429	G

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

Biological Unit 1 (5, 10)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_017419	P	25	L	PPB1_HUMAN	Polymorphism	1130335	A	P	3	L
2	UniProt	VAR_050520	I	89	L	PPB1_HUMAN	Polymorphism	13026692	A	I	67	L
3	UniProt	VAR_050521	R	231	P	PPB1_HUMAN	Polymorphism	1048988	A	R	209	P
4	UniProt	VAR_050522	R	263	H	PPB1_HUMAN	Polymorphism	2853378	A	R	241	H
5	UniProt	VAR_050523	E	451	G	PPB1_HUMAN	Polymorphism	1048994	A	E	429	G

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALKALINE_PHOSPHATASE	PS00123	Alkaline phosphatase active site.	PPB1_HUMAN	111-119	1	A:89-97

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALKALINE_PHOSPHATASE	PS00123	Alkaline phosphatase active site.	PPB1_HUMAN	111-119	2	A:89-97

Asymmetric Unit (11, 11)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000392027	1a	ENSE00001510465	chr2:233243244-233243588	345	PPB1_HUMAN	1-26	26	1	A:1-4	4
1.2	ENST00000392027	2	ENSE00001789454	chr2:233243681-233243797	117	PPB1_HUMAN	26-65	40	1	A:4-43	40
1.3	ENST00000392027	3	ENSE00001730171	chr2:233243910-233244025	116	PPB1_HUMAN	65-103	39	1	A:43-81	39
1.4a	ENST00000392027	4a	ENSE00001645266	chr2:233244223-233244397	175	PPB1_HUMAN	104-162	59	1	A:82-140	59
1.4c	ENST00000392027	4c	ENSE00001620414	chr2:233244474-233244646	173	PPB1_HUMAN	162-219	58	1	A:140-197	58
1.5	ENST00000392027	5	ENSE00001765153	chr2:233244896-233245030	135	PPB1_HUMAN	220-264	45	1	A:198-242	45
1.6	ENST00000392027	6	ENSE00001641289	chr2:233245130-233245202	73	PPB1_HUMAN	265-289	25	1	A:243-267	25
1.7	ENST00000392027	7	ENSE00001723793	chr2:233245333-233245467	135	PPB1_HUMAN	289-334	46	1	A:267-312	46
1.8	ENST00000392027	8	ENSE00001789464	chr2:233245550-233245741	192	PPB1_HUMAN	334-398	65	1	A:312-376	65
1.9b	ENST00000392027	9b	ENSE00001737846	chr2:233245961-233246077	117	PPB1_HUMAN	398-437	40	1	A:376-415	40
1.10b	ENST00000392027	10b	ENSE00001510464	chr2:233246207-233247599	1393	PPB1_HUMAN	437-535	99	1	A:415-480	66

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:480
 aligned with PPB1_HUMAN | P05187 from UniProtKB/Swiss-Prot  Length:535

    Alignment length:480
                                    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       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502
           PPB1_HUMAN    23 IIPVEEENPDFWNREAAEALGAAKKLQPAQTAAKNLIIFLGDGMGVSTVTAARILKGQKKDKLGPEIPLAMDRFPYVALSKTYNVDKHVPDSGATATAYLCGVKGNFQTIGLSAAARFNQCNTTRGNEVISVMNRAKKAGKSVGVVTTTRVQHASPAGTYAHTVNRNWYSDADVPASARQEGCQDIATQLISNMDIDVILGGGRKYMFRMGTPDPEYPDDYSQGGTRLDGKNLVQEWLAKRQGARYVWNRTELMQASLDPSVTHLMGLFEPGDMKYEIHRDSTLDPSLMEMTEAALRLLSRNPRGFFLFVEGGRIDHGHHESRAYRALTETIMFDDAIERAGQLTSEEDTLSLVTADHSHVFSFGGYPLRGSSIFGLAPGKARDRKAYTVLLYGNGPGYVLKDGARPDVTESESGSPEYRQQSAVPLDEETHAGEDVAVFARGPQAHLVHGVQEQTFIAHVMAFAACLEPYTACDLAPPA 502
               SCOP domains d1zeba_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1zebA00 A:1-480 Alkaline Phosphatase, subunit A                                                                                                                                                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains --------------------------------Alk_phosphatase-1zebA01 A:33-468                                                                                                                                                                                                                                                                                                                                                                                                                    ------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhh........eeeeeee...hhhhhhhhhhhhhhhh.........hhhhh.eeeeee.........hhhhhhhhhhhh.................hhhhh......hhhhhhhhh..eeeeeeeee..hhhhhh...........hhhhhhhhhhhh...hhhhhhhhh....eeeeehhhhhh...........hhhhh.......hhhhhhhhh...eeee.hhhhhhhhhhh....eeeee.......hhhhh......hhhhhhhhhhhhhh.....eeeeeee.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh....eeeeeee..ee.eee..........................eee................hhhhhh................ee...eeeeee..hhhhh..eee.hhhhhhhhhhh.hhhhh........ Sec.struct. author
                 SAPs(SNPs) --L---------------------------------------------------------------L---------------------------------------------------------------------------------------------------------------------------------------------P-------------------------------H-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G--------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------ALKALINE_----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.1a--------------------------------------Exon 1.3  PDB: A:43-81 UniProt: 65-103 Exon 1.4a  PDB: A:82-140 UniProt: 104-162                  ---------------------------------------------------------Exon 1.5  PDB: A:198-242 UniProt: 220-264    Exon 1.6  PDB: A:243-267 --------------------------------------------Exon 1.8  PDB: A:312-376 UniProt: 334-398                        --------------------------------------Exon 1.10b  PDB: A:415-480 UniProt: 437-535 [INCOMPLETE]           Transcript 1 (1)
           Transcript 1 (2) ---Exon 1.2  PDB: A:4-43 UniProt: 26-65    ------------------------------------------------------------------------------------------------Exon 1.4c  PDB: A:140-197 UniProt: 162-219                ---------------------------------------------------------------------Exon 1.7  PDB: A:267-312 UniProt: 289-334     ---------------------------------------------------------------Exon 1.9b  PDB: A:376-415               ----------------------------------------------------------------- Transcript 1 (2)
                 1zeb A   1 IIPVEEENPDFWNREAAEALGAAKKLQPAQTAAKNLIIFLGDGMGVSTVTAARILKGQKKDKLGPEIPLAMDRFPYVALSKTYNVDKHVPDsGATATAYLCGVKGNFQTIGLSAAARFNQCNTTRGNEVISVMNRAKKAGKSVGVVTTTRVQHASPAGTYAHTVNRNWYSDADVPASARQEGCQDIATQLISNMDIDVILGGGRKYMFRMGTPDPEYPDDYSQGGTRLDGKNLVQEWLAKRQGARYVWNRTELMQASLDPSVTHLMGLFEPGDMKYEIHRDSTLDPSLMEMTEAALRLLSRNPRGFFLFVEGGRIDHGHHESRAYRALTETIMFDDAIERAGQLTSEEDTLSLVTADHSHVFSFGGYPLRGSSIFGLAPGKARDRKAYTVLLYGNGPGYVLKDGARPDVTESESGSPEYRQQSAVPLDEETHAGEDVAVFARGPQAHLVHGVQEQTFIAHVMAFAACLEPYTACDLAPPA 480
                                    10        20        30        40        50        60        70        80        90 |     100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480
                                                                                                                      92-SEP

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: Alkaline phosphatase-like (78)

Superfamily: Alkaline phosphatase-like (78)

Family: Alkaline phosphatase (56)

Protein domain: automated matches (9)

Human (Homo sapiens) [TaxId: 9606] (7)

d1zeba_

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Alkaline Phosphatase, subunit A (66)

Homologous Superfamily: Alkaline Phosphatase, subunit A (66)

Human (Homo sapiens) (14)

1zebA00

A:1-480

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Alk_phosphatase (47)

Family: Alk_phosphatase (22)

Homo sapiens (Human) (6)

Alk_phosphatase-1zebA01

A:33-468

Asymmetric Unit(hide GO term definitions)

Chain A (PPB1_HUMAN | P05187)

molecular function
	GO:0004035	alkaline phosphatase activity	Catalysis of the reaction: an orthophosphoric monoester + H2O = an alcohol + phosphate, with an alkaline pH optimum.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	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:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016791	phosphatase activity	Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
	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:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
	GO:0031225	anchored component of membrane	The component of a membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric 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
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NAG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SEP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1zeb)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - 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
	1zeb
		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
	PPB1_HUMAN \| P05187
		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)
	3.1.3.1
		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
	PPB1_HUMAN \| P05187
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	PPB1_HUMAN \| P05187	:	1ew2 1zed 1zef 2glq 3mk0 3mk1 3mk2

1ew2	CRYSTAL STRUCTURE OF A HUMAN PHOSPHATASE
1zed
1zef

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 7)

Sites (6, 6)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (5, 5)

PROSITE Motifs (1, 1)

Exons (11, 11)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (15, 15)

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