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Title :   CRYSTAL STRUCTURE OF ALUMINUM-BOUND OVOTRANSFERRIN AT 2.15 ANGSTROM RESOLUTION

Authors :   K. Mizutani, B. Mikami, S. Aibara, M. Hirose

Date :   28 Sep 05 (Deposition) - 29 Nov 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

Chains :   Asym./Biol. Unit : A

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

Reference :   K. Mizutani, B. Mikami, S. Aibara, M. Hirose
Structure Of Aluminium-Bound Ovotransferrin At 2. 15 Angstroms Resolution.
Acta Crystallogr. , Sect. D V. 61 1636 2005
PubMed-ID: 16301797 | Reference-DOI: 10.1107/S090744490503266X
(for further references see the PDB file header)

Molecule 1 - OVOTRANSFERRIN
	Chains	:	A
	Organism Common	:	CHICKEN
	Organism Scientific	:	GALLUS GALLUS
	Organism Taxid	:	9031
	Synonym	:	CONALBUMIN, ALLERGEN GAL D 3, GAL D III, SERUM TRANSFERRIN
	Tissue	:	EGG WHITE

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	AL	2	Ligand/Ion	ALUMINUM ION
2	BCT	2	Ligand/Ion	BICARBONATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:60 , TYR A:92 , TYR A:191 , HIS A:250 , BCT A:688	BINDING SITE FOR RESIDUE AL A 687
2	AC2	SOFTWARE	ASP A:60 , TYR A:92 , THR A:117 , ARG A:121 , SER A:122 , ALA A:123 , GLY A:124 , TYR A:191 , HIS A:250 , AL A:687	BINDING SITE FOR RESIDUE BCT A 688
3	AC3	SOFTWARE	ASP A:395 , TYR A:431 , TYR A:524 , HIS A:592 , BCT A:690	BINDING SITE FOR RESIDUE AL A 689
4	AC4	SOFTWARE	ASP A:395 , TYR A:431 , THR A:456 , ARG A:460 , THR A:461 , ALA A:462 , GLY A:463 , TYR A:524 , HIS A:592 , AL A:689	BINDING SITE FOR RESIDUE BCT A 690

Asymmetric/Biological Unit

No.	Residues
1	A:10	-	A:45
2	A:20	-	A:36
3	A:115	-	A:197
4	A:160	-	A:174
5	A:171	-	A:182
6	A:228	-	A:242
7	A:348	-	A:380
8	A:358	-	A:371
9	A:405	-	A:680
10	A:421	-	A:643
11	A:454	-	A:530
12	A:478	-	A:671
13	A:488	-	A:502
14	A:499	-	A:513
15	A:570	-	A:584

Asymmetric/Biological Unit

No.	Residues
1	Ala A:70	-	Pro A:71
2	Gly A:286	-	Pro A:287
3	Ile A:508	-	Pro A:509

Asymmetric/Biological Unit (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_TRFE_CHICK_001 *	A	83	V	TRFE_CHICK	---	---	A	V	64	V
2	UniProt	VAR_TRFE_CHICK_002 *	V	100	I	TRFE_CHICK	---	---	A	V	81	I
3	UniProt	VAR_TRFE_CHICK_003 *	R	154	W	TRFE_CHICK	---	---	A	R	135	W
4	UniProt	VAR_TRFE_CHICK_004 *	S	686	N	TRFE_CHICK	---	---	A	S	667	N
	* ID not provided by source

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

Asymmetric/Biological Unit (4, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRANSFERRIN_LIKE_4	PS51408	Transferrin-like domain profile.	TRFE_CHICK	26-352 364-689	2	A:7-333 A:345-670
2	TRANSFERRIN_LIKE_1	PS00205	Transferrin-like domain signature 1.	TRFE_CHICK	111-120 450-459	2	A:92-101 A:431-440
3	TRANSFERRIN_LIKE_2	PS00206	Transferrin-like domain signature 2.	TRFE_CHICK	210-226 543-558	2	A:191-207 A:524-539
4	TRANSFERRIN_LIKE_3	PS00207	Transferrin-like domain signature 3.	TRFE_CHICK	242-272 584-614	2	A:223-253 A:565-595

(no "Exon" information available for 2D3I)

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:670
 aligned with TRFE_CHICK | P02789 from UniProtKB/Swiss-Prot  Length:705

    Alignment length:682
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703  
           TRFE_CHICK    24 SVIRWCTISSPEEKKCNNLRDLTQQERISLTCVQKATYLDCIKAIANNEADAISLDGGQAFEAGLAPYKLKPIAAEVYEHTEGSTTSYYAVAVVKKGTEFTVNDLQGKTSCHTGLGRSAGWNIPIGTLLHRGAIEWEGIESGSVEQAVAKFFSASCVPGATIEQKLCRQCKGDPKTKCARNAPYSGYSGAFHCLKDGKGDVAFVKHTTVNENAPDQKDEYELLCLDGSRQPVDNYKTCNWARVAAHAVVARDDNKVEDIWSFLSKAQSDFGVDTKSDFHLFGPPGKKDPVLKDLLFKDSAIMLKRVPSLMDSQLYLGFEYYSAIQSMRKDQLTPSPRENRIQWCAVGKDEKSKCDRWSVVSNGDVECTVVDETKDCIIKIMKGEADAVALDGGLVYTAGVCGLVPVMAERYDDESQCSKTDERPASYFAVAVARKDSNVNWNNLKGKKSCHTAVGRTAGWVIPMGLIHNRTGTCNFDEYFSEGCAPGSPPNSRLCQLCQGSGGIPPEKCVASSHEKYFGYTGALRCLVEKGDVAFIQHSTVEENTGGKNKADWAKNLQMDDFELLCTDGRRANVMDYRECNLAEVPTHAVVVRPEKANKIRDLLERQEKRFGVNGSEKSKFMMFESQNKDLLFKDLTKCLFKVREGTTYKEFLGDKFYTVISSLKTCNPSDILQMCSFLEGK 705
               SCOP domains d2d3ia1 A:5-333 automated matches                                                                                                                                                                                                                                                                                                        d2      d3ia2 A:334-686 automated matches                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2d3iA01 A:5-91,A:248-335 Periplasmic binding protein-like II                           2d3iA02 A:92-247 Periplasmic binding protein-like II                                                                                                        2d3iA01 A:5-91,A:248-335 Periplasmic binding protein-like II                                  2d3iA03 A:342-430,A:590-685 Periplasmic binding protein-like II                          2d3iA04 A:431-589 Periplasmic binding protein-like II                                                                                                          2d3iA03 A:342-430,A:590-685 Periplasmic binding protein-like II                                 - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.hhhhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhh.....eeehhhhhhhhhh.....eeeeeee.........eeeeeeeee.....hhhhh...eeee........hhhhhhhhhhh......hhhhhhhhhhhhhhh.eee......hhhhh.................hhhhhhhhhhhh....eeeee.hhhhhhhhhhhh.eeee.....eehhhhhhhh..eeee..eeee....hhhhhhhhhhhhhhhhh................hhhhh.........eeee.....hhhhhhhhhhhhhhhhh....------...eeeeeehhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhh....eeehhhhhhhhhhh..eeeeeee..hhhhh------...eeeeeeee.............eeee........hhhhhhhhhhhhh..hhhhh..eee.......hhhhh.....................hhhhhhhhhhhhh..eeeee.hhhhhh.............hhh.eeee.....eee.hhhhhh..eee...eeeehhhhhhhhhhhhhhhhhhhh..........................eeee.....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------V----------------I-----------------------------------------------------W---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------N------------------- SAPs(SNPs)
                PROSITE (1) --TRANSFERRIN_LIKE_4  PDB: A:7-333 UniProt: 26-352                                                                                                                                                                                                                                                                                       -----------TRANSFERRIN_LIKE_4  PDB: A:345-670 UniProt: 364-689                                                                                                                                                                                                                                                                                   ---------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------TRANSFERRI-----------------------------------------------------------------------------------------TRANSFERRIN_LIKE_---------------TRANSFERRIN_LIKE_3             ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRANSFERRI-----------------------------------------------------------------------------------TRANSFERRIN_LIKE-------------------------TRANSFERRIN_LIKE_3             ------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d3i A   5 SVIRWCTISSPEEKKCNNLRDLTQQERISLTCVQKATYLDCIKAIANNEADAISLDGGQVFEAGLAPYKLKPIAAEVYEHTEGSTTSYYAVAVVKKGTEFTVNDLQGKTSCHTGLGRSAGWNIPIGTLIHRGAIEWEGIESGSVEQAVAKFFSASCVPGATIEQKLCRQCKGDPKTKCARNAPYSGYSGAFHCLKDGKGDVAFVKHTTVNENAPDQKDEYELLCLDGSRQPVDNYKTCNWARVAAHAVVARDDNKVEDIWSFLSKAQSDFGVDTKSDFHLFGPPGKKDPVLKDLLFKDSAIMLKRVPSLMDSQLYLGFEYYSAIQSMRKDQ------ENRIQWCAVGKDEKSKCDRWSVVSNGDVECTVVDETKDCIIKIMKGEADAVALDGGLVYTAGVCGLVPVMAERYDDESQC------PASYFAVAVARKDSNVNWNNLKGKKSCHTAVGRTAGWVIPMGLIHNRTGTCNFDEYFSEGCAPGSPPNSRLCQLCQGSGGIPPEKCVASSHEKYFGYTGALRCLVEKGDVAFIQHSTVEENTGGKNKADWAKNLQMDDFELLCTDGRRANVMDYRECNLAEVPTHAVVVRPEKANKIRDLLERQEKRFGVNGSEKSKFMMFESQNKDLLFKDLTKCLFKVREGTTYKEFLGDKFYTVISSLKTCNPSDILQMCSFLEGK 686
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334|      344       354       364       374       384       394       404       414      |  -   |   434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684  
                                                                                                                                                                                                                                                                                                                                                                    335    342                                                                            421    428

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: automated matches (267)

Protein domain: automated matches (267)

Chicken (Gallus gallus) [TaxId: 9031] (1)

1a	d2d3ia1	A:5-333
1b	d2d3ia2	A:334-686

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)

Chicken (Gallus gallus) (10)

1a	2d3iA02	A:92-247
1b	2d3iA04	A:431-589
1c	2d3iA01	A:5-91,A:248-335
1d	2d3iA03	A:342-430,A:590-685

(no "Pfam Domain" information available for 2D3I)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TRFE_CHICK | P02789)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0006953	acute-phase response	An acute inflammatory response that involves non-antibody proteins whose concentrations in the plasma increase in response to infection or injury of homeothermic animals.
	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:0032496	response to lipopolysaccharide	Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
	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:0031012	extracellular matrix	A structure lying external to one or more cells, which provides structural support for cells or tissues.
	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
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		Ala A:70 - Pro A:71	[ RasMol ]
		Gly A:286 - Pro A:287	[ RasMol ]
		Ile A:508 - Pro A:509	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (15, 15)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

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