1GVC - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   18KDA N-II DOMAIN FRAGMENT OF DUCK OVOTRANSFERRIN + NTA

Authors :   P. Kuser, D. R. Hall, M. L. Haw, M. Neu, P. F. Lindley

Date :   07 Feb 02 (Deposition) - 12 Feb 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A

Keywords :   Iron Transport, Glycoprotein, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Kuser, D. R. Hall, M. L. Haw, M. Neu, R. Evans, P. F. Lindley
The Mechanism Of Iron Uptake By Transferrins: The X-Ray Structures Of The 18 Kda Nii Domain Fragment Of Duck Ovotransferrin And Its Nitrilotriacetate Complex
Acta Crystallogr. , Sect. D V. 58 777 2002
PubMed-ID: 11976488 | Reference-DOI: 10.1107/S0907444902003724

Molecule 1 - OVOTRANSFERRIN
	Chains	:	A
	Fragment	:	N-II FRAGMENT, RESIDUES 91-247
	Organism Common	:	COMMON DUCK
	Organism Scientific	:	ANAS PLATYRHYNCHOS
	Organism Taxid	:	8839
	Other Details	:	COMPLEX OF DUCK OVOTRANSFERRIN FRAGMENT AND NTA

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 3)

No.	Name	Count	Type	Full Name
1	CO3	1	Ligand/Ion	CARBONATE ION
2	FE	1	Ligand/Ion	FE (III) ION
3	NTA	1	Ligand/Ion	NITRILOTRIACETIC ACID

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:95 , THR A:120 , ARG A:124 , SER A:125 , ALA A:126 , GLY A:127 , TYR A:194 , NTA A:1252 , FE A:1253	BINDING SITE FOR RESIDUE CO3 A1251
2	AC2	SOFTWARE	TYR A:194 , CO3 A:1251 , NTA A:1252	BINDING SITE FOR RESIDUE FE A1253
3	AC3	SOFTWARE	TYR A:95 , ARG A:124 , SER A:125 , TYR A:194 , CO3 A:1251 , FE A:1253 , HOH A:2006 , HOH A:2096	BINDING SITE FOR RESIDUE NTA A1252

Asymmetric/Biological Unit

No.	Residues
1	A:118	-	A:200
2	A:163	-	A:177
3	A:174	-	A:185
4	A:231	-	A:245

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

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

Asymmetric/Biological Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRANSFERRIN_LIKE_1	PS00205	Transferrin-like domain signature 1.	TRFE_ANAPL	92-101 431-440	1	A:95-104 -
2	TRANSFERRIN_LIKE_2	PS00206	Transferrin-like domain signature 2.	TRFE_ANAPL	191-207 524-539	1	A:194-210 -
3	TRANSFERRIN_LIKE_3	PS00207	Transferrin-like domain signature 3.	TRFE_ANAPL	223-253	1	A:226-250

(no "Exon" information available for 1GVC)

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:157
 aligned with TRFE_ANAPL | P56410 from UniProtKB/Swiss-Prot  Length:686

    Alignment length:157
                                   100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       
           TRFE_ANAPL    91 SYYAVAVVKKGTDFMIKDLRGKTSCHTGLGRSAGWNIPIGTLIHREDIEWEGIESGISEQAVAKFFSASCVPGATIEQKLCRQCKGDAKTKCLRNGPYSGYSGAFQCLKDGKGDVAFVKHTTVQENAPEEKDEYELLCLDGSRQPVDSYKTCNWARV 247
               SCOP domains d1gvca_ A: Ovotransferrin                                                                                                                                     SCOP domains
               CATH domains 1gvcA00 A:94-250 Periplasmic binding protein-like II                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhh...eeee........hhhhhhhhhhh...........hhhhhhhhhh.eee......hhhhhh................hhhhhhhhhhhh....eeeee.hhhhhhhhhhhh.eeee.....eee.hhhhhh..eee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -TRANSFERRI-----------------------------------------------------------------------------------------TRANSFERRIN_LIKE_---------------TRANSFERRIN_LIKE_3        PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gvc A  94 SYYAVAVVKKGTDFMIKDLRGKTSCHTGLGRSAGWNIPIGTLIHRGDIEWEGIESGSVEQAVAKFFSASCVPGATTEQKLCRQCKGDAKTKCLRNAPYSGYSGAFQCLKDGKGDVAFVKHTTVQENAPEEKDEYELLCLDGTRQPVDSYKTCNWARV 250
                                   103       113       123       133       143       153       163       173       183       193       203       213       223       233       243

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Periplasmic binding protein-like II (813)

Superfamily: Periplasmic binding protein-like II (813)

Family: Transferrin (82)

Protein domain: Ovotransferrin (14)

Duck (Anas platyrhynchos) [TaxId: 8839] (5)

d1gvca_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: D-Maltodextrin-Binding Protein; domain 2 (600)

Homologous Superfamily: Periplasmic binding protein-like II (486)

Common duck (Anas platyrhynchos) (2)

1gvcA00

A:94-250

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TRFE_ANAPL | P56410)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0006811	ion transport	The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0055072	iron ion homeostasis	Any process involved in the maintenance of an internal steady state of iron ions within an organism or cell.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
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/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
		CO3	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NTA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

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

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
	1gvc
		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
	TRFE_ANAPL \| P56410
		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)
	(no 'Enzyme Classificator' available)
		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
	TRFE_ANAPL \| P56410
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	TRFE_ANAPL \| P56410	:	1aov 1dot 1gv8 1ovb

1aov	APO DUCK OVOTRANSFERRIN
1dot	DUCK OVOTRANSFERRIN
1gv8	18 KDA FRAGMENT OF N-II DOMAIN OF DUCK OVOTRANSFERRIN
1ovb	OVOTRANSFERRIN (18 KDA FRAGMENT, DOMAIN II FROM N-TERMINAL LOBE)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

SS Bonds (4, 4)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 3)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (6, 6)

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