1JNF - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

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

Title :   RABBIT SERUM TRANSFERRIN AT 2.6 A RESOLUTION.

Authors :   D. R. Hall, J. M. Hadden, G. A. Leonard, S. Bailey, M. Neu, M. Winn, P. F. Lindley

Date :   24 Jul 01 (Deposition) - 01 Aug 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym./Biol. Unit : A

Keywords :   Beta-Alpha Protein, Bilobal, Iron Transport, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. R. Hall, J. M. Hadden, G. A. Leonard, S. Bailey, M. Neu, M. Winn, P. F. Lindley
The Crystal And Molecular Structures Of Diferric Porcine And Rabbit Serum Transferrins At Resolutions Of 2. 15 And 2. 60 A, Respectively.
Acta Crystallogr. , Sect. D V. 58 70 2002
PubMed-ID: 11752780 | Reference-DOI: 10.1107/S0907444901017309
(for further references see the PDB file header)

Molecule 1 - SEROTRANSFERRIN
	Chains	:	A
	Organism Common	:	RABBIT
	Organism Scientific	:	ORYCTOLAGUS CUNICULUS
	Organism Taxid	:	9986
	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	CL	1	Ligand/Ion	CHLORIDE ION
2	CO3	2	Ligand/Ion	CARBONATE ION
3	FE	2	Ligand/Ion	FE (III) ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:63 , TYR A:95 , THR A:120 , ARG A:124 , ALA A:126 , GLY A:127 , TYR A:188 , HIS A:249 , FE A:702	BINDING SITE FOR RESIDUE CO3 A 700
2	AC2	SOFTWARE	ASP A:392 , TYR A:425 , THR A:451 , ARG A:455 , THR A:456 , ALA A:457 , GLY A:458 , TYR A:514 , HIS A:582 , FE A:703	BINDING SITE FOR RESIDUE CO3 A 701
3	AC3	SOFTWARE	ASP A:63 , TYR A:95 , TYR A:188 , HIS A:249 , CO3 A:700	BINDING SITE FOR RESIDUE FE A 702
4	AC4	SOFTWARE	ASP A:392 , TYR A:425 , TYR A:514 , HIS A:582 , CO3 A:701	BINDING SITE FOR RESIDUE FE A 703
5	AC5	SOFTWARE	ARG A:124 , GLY A:187 , TYR A:188 , HOH A:803	BINDING SITE FOR RESIDUE CL A 800

Asymmetric/Biological Unit

No.	Residues
1	A:9	-	A:48
2	A:19	-	A:39
3	A:118	-	A:194
4	A:137	-	A:331
5	A:158	-	A:174
6	A:161	-	A:179
7	A:171	-	A:177
8	A:227	-	A:241
9	A:339	-	A:593
10	A:345	-	A:377
11	A:355	-	A:368
12	A:402	-	A:671
13	A:417	-	A:634
14	A:449	-	A:520
15	A:473	-	A:662
16	A:483	-	A:497
17	A:494	-	A:503
18	A:560	-	A:574
19	A:612	-	A:617

Asymmetric/Biological Unit

No.	Residues
1	Thr A:73	-	Pro A:74
2	Lys A:144	-	Pro A:145

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_TRFE_RABIT_001 *	V	517	I	TRFE_RABIT	---	---	A	V	498	I
	* ID not provided by source

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

Asymmetric/Biological Unit (4, 7)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRANSFERRIN_LIKE_4	PS51408	Transferrin-like domain profile.	TRFE_RABIT	25-347 361-680	2	A:6-328 A:342-661
2	TRANSFERRIN_LIKE_2	PS00206	Transferrin-like domain signature 2.	TRFE_RABIT	207-223 533-548	2	A:188-204 A:514-529
3	TRANSFERRIN_LIKE_3	PS00207	Transferrin-like domain signature 3.	TRFE_RABIT	241-271 574-604	2	A:222-252 A:555-585
4	TRANSFERRIN_LIKE_1	PS00205	Transferrin-like domain signature 1.	TRFE_RABIT	444-453	1	A:425-434

(no "Exon" information available for 1JNF)

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:674
 aligned with TRFE_RABIT | P19134 from UniProtKB/Swiss-Prot  Length:695

    Alignment length:674
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691    
           TRFE_RABIT    22 EKTVRWCAVNDHEASKCANFRDSMKKVLPEDGPRIICVKKASYLDCIKAIAAHEADAVTLDAGLVHEAGLTPNNLKPVVAEFYGSKENPKTFYYAVALVKKGSNFQLNELQGKKSCHTGLGRSAGWNIPIGLLYCDLPEPRKPLEKAVASFFSGSCVPCADGADFPQLCQLCPGCGCSSVQPYFGYSGAFKCLKDGLGDVAFVKQETIFENLPSKDERDQYELLCLDNTRKPVDEYEQCHLARVPSHAVVARSVDGKEDLIWELLNQAQEHFGKDKSGDFQLFSSPHGKNLLFKDSAYGFFKVPPRMDANLYLGYEYVTAVRNLREGICPDPLQDECKAVKWCALSHHERLKCDEWSVTSGGLIECESAETPEDCIAKIMNGEADAMSLDGGYVYIAGQCGLVPVLAENYESTDCKKAPEEGYLSVAVVKKSNPDINWNNLEGKKSCHTAVDRTAGWNIPMGLLYNRINHCRFDEFFRQGCAPGSQKNSSLCELCVGPSVCAPNNREGYYGYTGAFRCLVEKGDVAFVKSQTVLQNTGGRNSEPWAKDLKEEDFELLCLDGTRKPVSEAHNCHLAKAPNHAVVSRKDKAACVKQKLLDLQVEYGNTVADCSSKFCMFHSKTKDLLFRDDTKCLVDLRGKNTYEKYLGADYIKAVSNLRKCSTSRLLEACTFHKH 695
               SCOP domains d1jnfa1 A:3-334 Transferrin                                                                                                                                                                                                                                                                                                                 d1jnfa2 A:335-676 Transferrin                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1jnfA01 A:3-94,A:247-336 Periplasmic binding protein-like II                                1jnfA02 A:95-246 Periplasmic binding protein-like II                                                                                                    1jnfA01 A:3-94,A:247-336 Periplasmic binding protein-like II                              1jnfA03 A:337-424,A:580-676 Periplasmic binding protein-like II                         1jnfA04 A:425-579 Periplasmic binding protein-like II                                                                                                      1jnfA03 A:337-424,A:580-676 Periplasmic binding protein-like II                                   CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Transferrin-1jnfA01 A:342-661                                                                                                                                                                                                                                                                                                   --------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Transferrin-1jnfA02 A:342-661                                                                                                                                                                                                                                                                                                   --------------- Pfam domains (2)
         Sec.struct. author ..eeeeeeehhhhhhhhhhhhhhhhhhh.....eeeeeee.hhhhhhhhhhh.....eeehhhhhhhhhh....eeeeeeee.........eeeeeeeee.....hhhhh....eee........hhhhhhhhhhhh.....hhhhhhhhhh..ee........hhhhhh.............hhhhhhhhhhhh....eeeee.hhhhhhh.hhhhhh.eeee.....eee.hhh.....eeee..eeeee....hhhhhhhhhhhhhhhhh.........................eeee.....hhhhhhhhhhhhhhhhhhh.............eeeeeehhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh.....eeehhhhhhhhhhh..eeeeeee.............eeeeeeee......hhhhh...eeee........hhhhhhhhhhhhh..hhhhhh.eee.......hhhhh................hhhhhhhhhhhhh..eeeee.hhhhhhh............hhh.eeee.....eee.hhhhhh..eee...eeee...hhhhhhhhhhhhhhhhh...........................eeee.....hhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------I---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---TRANSFERRIN_LIKE_4  PDB: A:6-328 UniProt: 25-347                                                                                                                                                                                                                                                                                   -------------TRANSFERRIN_LIKE_4  PDB: A:342-661 UniProt: 361-680                                                                                                                                                                                                                                                                             --------------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRANSFERRIN_LIKE_-----------------TRANSFERRIN_LIKE_3             ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRANSFERRI-------------------------------------------------------------------------------TRANSFERRIN_LIKE-------------------------TRANSFERRIN_LIKE_3             ------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jnf A   3 EKTVRWCAVNDHEASKCANFRDSMKKVLPEDGPRIICVKKASYLDCIKAIAAHEADAVTLDAGLVHEAGLTPNNLKPVVAEFYGSKENPKTFYYAVALVKKGSNFQLNELQGKKSCHTGLGRSAGWNIPIGLLLCDLPEPRKPLEKAVASFFSGSCVPCADGADFPQLCQLCPGCGCSSVQPYFGYSGAFKCLKDGLGDVAFVKQETIFENLPSKDERDQYELLCLDNTRKPVDEYEQCHLARVPSHAVVARSVDGKEDLIWELLNQAQEHFGKDKSGDFQLFSSPHGKNLLFKDSAYGFFKVPPRMDANLYLGYEYVTAVRNLREGICPDPLQDECKAVKWCALGHHERLKCDEWSVTSGGLIECESAETPEDCIAKIMNGEADAMSLDGGYVYIAGQCGLVPVLAENYESTDCKKAPEEGYLSVAVVKKSNPDINWNNLEGKKSCHTAVDRTAGWNIPMGLLYNRINHCRFDEFFRQGCAPGSQKNSSLCELCVGPSVCAPNNREGYYGYTGAFRCLVEKGDVAFVKSQTVLQNTGGRNSEPWAKDLKEEDFELLCLDGTRKPVSEAHNCHLAKAPNHAVVSRKDKAACVKQKLLDLQVEFGNTVADCSSKFCMFHSKTKDLLFRDDTKCLVDLRGKNTYEKYLGADYIKAVSNLRKCSTSRLLEACTFHKH 676
                                    12        22        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

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: Transferrin (23)

Rabbit (Oryctolagus cuniculus) [TaxId: 9986] (2)

1a	d1jnfa1	A:3-334
1b	d1jnfa2	A:335-676

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)

Rabbit (Oryctolagus cuniculus) (2)

1a	1jnfA02	A:95-246
1b	1jnfA04	A:425-579
1c	1jnfA01	A:3-94,A:247-336
1d	1jnfA03	A:337-424,A:580-676

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PBP (391)

Family: Transferrin (53)

Oryctolagus cuniculus (Rabbit) (2)

1a	Transferrin-1jnfA01	A:342-661
1b	Transferrin-1jnfA02	A:342-661

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TRFE_RABIT | P19134)

molecular function
	GO:0008199	ferric iron binding	Interacting selectively and non-covalently with ferric iron, Fe(III).
	GO:0015091	ferric iron transmembrane transporter activity	Enables the transfer of ferric iron (Fe(III) or Fe3+) ions from one side of a membrane to the other.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0006879	cellular iron ion homeostasis	Any process involved in the maintenance of an internal steady state of iron ions at the level of a cell.
	GO:0015682	ferric iron transport	The directed movement of ferric iron (Fe(III) or Fe3+) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	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:0006826	iron ion transport	The directed movement of iron (Fe) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	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:0005623	cell	The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
	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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(no "Related Entries Specified in the PDB File" available for 1JNF)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (19, 19)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

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Exons (0, 0)

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