1N04 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   DIFERRIC CHICKEN SERUM TRANSFERRIN AT 2.8 A RESOLUTION.

Authors :   P. Guha Thakurta, D. Choudhury, R. Dasgupta, J. K. Dattagupta

Date :   11 Oct 02 (Deposition) - 30 Sep 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym./Biol. Unit : A

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

Reference :   P. Guha Thakurta, D. Choudhury, R. Dasgupta, J. K. Dattagupta
Structure Of Diferric Hen Serum Transferrin At 2. 8 A Resolution.
Acta Crystallogr. , Sect. D V. 59 1773 2003
PubMed-ID: 14501117 | Reference-DOI: 10.1107/S0907444903016652
(for further references see the PDB file header)

Molecule 1 - SERUM TRANSFERRIN
	Chains	:	A
	Organism Common	:	CHICKEN
	Organism Scientific	:	GALLUS GALLUS
	Organism Taxid	:	9031
	Synonym	:	OVOTRANSFERRIN
	Tissue	:	SERUM

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 5)

No.	Name	Count	Type	Full Name
1	CO3	2	Ligand/Ion	CARBONATE ION
2	FE	2	Ligand/Ion	FE (III) ION
3	FUL	1	Ligand/Ion	BETA-L-FUCOSE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:8 , ASN A:52	BINDING SITE FOR RESIDUE FUL A 691
2	AC2	SOFTWARE	ASP A:60 , TYR A:92 , TYR A:191 , HIS A:250 , CO3 A:689	BINDING SITE FOR RESIDUE FE A 687
3	AC3	SOFTWARE	ASP A:395 , TYR A:431 , TYR A:524 , HIS A:592 , CO3 A:690	BINDING SITE FOR RESIDUE FE A 688
4	AC4	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 , FE A:687	BINDING SITE FOR RESIDUE CO3 A 689
5	AC5	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 , FE A:688	BINDING SITE FOR RESIDUE CO3 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

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	A	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 1N04)

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:683
 aligned with TRFE_CHICK | P02789 from UniProtKB/Swiss-Prot  Length:705

    Alignment length:683
                                    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       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702   
           TRFE_CHICK    23 KSVIRWCTISSPEEKKCNNLRDLTQQERISLTCVQKATYLDCIKAIANNEADAISLDGGQAFEAGLAPYKLKPIAAEVYEHTEGSTTSYYAVAVVKKGTEFTVNDLQGKTSCHTGLGRSAGWNIPIGTLLHRGAIEWEGIESGSVEQAVAKFFSASCVPGATIEQKLCRQCKGDPKTKCARNAPYSGYSGAFHCLKDGKGDVAFVKHTTVNENAPDQKDEYELLCLDGSRQPVDNYKTCNWARVAAHAVVARDDNKVEDIWSFLSKAQSDFGVDTKSDFHLFGPPGKKDPVLKDLLFKDSAIMLKRVPSLMDSQLYLGFEYYSAIQSMRKDQLTPSPRENRIQWCAVGKDEKSKCDRWSVVSNGDVECTVVDETKDCIIKIMKGEADAVALDGGLVYTAGVCGLVPVMAERYDDESQCSKTDERPASYFAVAVARKDSNVNWNNLKGKKSCHTAVGRTAGWVIPMGLIHNRTGTCNFDEYFSEGCAPGSPPNSRLCQLCQGSGGIPPEKCVASSHEKYFGYTGALRCLVEKGDVAFIQHSTVEENTGGKNKADWAKNLQMDDFELLCTDGRRANVMDYRECNLAEVPTHAVVVRPEKANKIRDLLERQEKRFGVNGSEKSKFMMFESQNKDLLFKDLTKCLFKVREGTTYKEFLGDKFYTVISSLKTCNPSDILQMCSFLEGK 705
               SCOP domains d1n04a1 A:4-334 Ovotransferrin                                                                                                                                                                                                                                                                                                             d1n04a2 A:335-686 Ovotransferrin                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -1n04A01 A:5-91,A:248-339 Periplasmic binding protein-like II                           1n04A02 A:92-247 Periplasmic binding protein-like II                                                                                                        1n04A01 A:5-91,A:248-339 Periplasmic binding protein-like II                                1n04A03 A:340-430,A:590-685 Periplasmic binding protein-like II                            1n04A04 A:431-589 Periplasmic binding protein-like II                                                                                                          1n04A03 A:340-430,A:590-685 Periplasmic binding protein-like II                                 - CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Transferrin-1n04A01 A:345-670                                                                                                                                                                                                                                                                                                         ---------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Transferrin-1n04A02 A:345-670                                                                                                                                                                                                                                                                                                         ---------------- Pfam domains (2)
         Sec.struct. author ..eeeeee.hhhhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhh......eehhhhhhhhh......eeeeeeee........eeeeeeeee.....hhhhh....eee........hhhhhhhhhhh...........hhhhhhhhhh..ee......hhhhhh................hhhhhhhhhhhh.....eeee.......hhhhhh.eeee.....eehhhhhhhh..eeee..eeee.....hhhhhhhhhhhhhhhh................hhhhh.......eeeeee.....hhhhhhhhhhhhhhhhh.............eeeeeehhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhh.....eeehhhhhhhhhhh..eeeeeee...............eeeeeeeee.............eee.........hhhhhhhhhhhh....hhhhh.eee.......hhhhhh.....................hhhhhhhhhhh...eeeee.hhhhhhh.......hhhhh....eeee.....ee..........eeee..eeeehhhhhhhhhhhhhhhhhhhh..........................eeee.....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhh.. 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
                 1n04 A   4 KSVIRWCTISSPEEKKCNNLRDLTQQERISLTCVQKATYLDCIKAIANNEADAISLDGGQAFEAGLAPYKLKPIAAEVYEHTEGSTTSYYAVAVVKKGTEFTVNDLQGKTSCHTGLGRSAGWNIPIGTLLHRGAIEWEGIESGSVEQAVAKFFSASCVPGATIEQKLCRQCKGDPKTKCARNAPYSGYSGAFHCLKDGKGDVAFVKHTTVNENAPDQKDEYELLCLDGSRQPVDNYKTCNWARVAAHAVVARDDNKVEDIWSFLSKAQSDFGVDTKSDFHLFGPPGKKDPVLKDLLFKDSAIMLKRVPSLMDSQLYLGFEYYSAIQSMRKDQLTPSPRENRIQWCAVGKDEKSKCDRWSVVSNGDVECTVVDETKDCIIKIMKGEADAVALDGGLVYTAGVCGLVPVMAERYDDESQCSKTDERPASYFAVAVARKDSNVNWNNLKGKKSCHTAVGRTAGWVIPMGLIHNRTGTCNFDEYFSEGCAPGSPPNSRLCQLCQGSGGIPPEKCVASSHEKYFGYTGALRCLVEKGDVAFIQHSTVEENTGGKNKADWAKNLQMDDFELLCTDGRRANVMDYRECNLAEVPTHAVVVRPEKANKIRDLLERQEKRFGVNGSEKSKFMMFESQNKDLLFKDLTKCLFKVREGTTYKEFLGDKFYTVISSLKTCNPSDILQMCSFLEGK 686
                                    13        23        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

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)

Chicken (Gallus gallus) [TaxId: 9031] (9)

1a	d1n04a1	A:4-334
1b	d1n04a2	A:335-686

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	1n04A02	A:92-247
1b	1n04A04	A:431-589
1c	1n04A01	A:5-91,A:248-339
1d	1n04A03	A:340-430,A:590-685

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PBP (391)

Family: Transferrin (53)

Gallus gallus (Chicken) (7)

1a	Transferrin-1n04A01	A:345-670
1b	Transferrin-1n04A02	A:345-670

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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	Cis Peptide Bonds
		Ala A:70 - Pro A:71	[ RasMol ]
		Gly A:286 - Pro A:287	[ RasMol ]

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	1n04
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	TRFE_CHICK \| P02789	:	1aiv 1d9k 1iej 1iq7 1jl4 1nft 1nnt 1ovt 1ryx 1tfa 2d3i

(no "Related Entries Specified in the PDB File" available for 1N04)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (15, 15)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (4, 4)

PROSITE Motifs (4, 8)

Exons (0, 0)

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