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Title :   STRUCTURE OF DIFERRIC BUFFALO LACTOFERRIN

Authors :   S. Karthikeyan, S. Yadav, T. P. Singh

Date :   21 Jun 98 (Deposition) - 13 Jan 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.37

Chains :   Asym./Biol. Unit : A

Keywords :   Iron Binding Protein, Lactoferrin, Structure, Antibacterial, Iron-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Karthikeyan, S. Yadav, M. Paramasivam, A. Srinivasan, T. P. Singh
Structure Of Buffalo Lactoferrin At 3. 3 A Resolution At 277 K.
Acta Crystallogr. , Sect. D V. 56 684 2000
PubMed-ID: 10818344 | Reference-DOI: 10.1107/S0907444900005151
(for further references see the PDB file header)

Molecule 1 - LACTOFERRIN
	Cellular Location	:	EXTRACELLULAR
	Chains	:	A
	Organism Common	:	WATER BUFFALO
	Organism Scientific	:	BUBALUS BUBALIS
	Organism Taxid	:	89462
	Secretion	:	MILK

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

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

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:60 , TYR A:92 , TYR A:192 , HIS A:253 , CO3 A:692	BINDING SITE FOR RESIDUE FE A 690
2	AC2	SOFTWARE	ASP A:395 , TYR A:433 , TYR A:526 , HIS A:595 , CO3 A:693	BINDING SITE FOR RESIDUE FE A 691
3	AC3	SOFTWARE	ASP A:60 , TYR A:92 , THR A:117 , ARG A:121 , ALA A:123 , GLY A:124 , TYR A:192 , HIS A:253 , FE A:690	BINDING SITE FOR RESIDUE CO3 A 692
4	AC4	SOFTWARE	ASP A:395 , TYR A:433 , THR A:459 , ARG A:463 , THR A:464 , ALA A:465 , GLY A:466 , TYR A:526 , HIS A:595 , FE A:691	BINDING SITE FOR RESIDUE CO3 A 693
5	FE1	UNKNOWN	ASP A:60 , TYR A:92 , TYR A:192 , HIS A:253 , CO3 A:692	IRON BINDING SITE IN N-LOBE.
6	FE2	UNKNOWN	ASP A:395 , TYR A:433 , TYR A:526 , HIS A:595 , CO3 A:693	IRON BINDING SITE IN C-LOBE.

Asymmetric/Biological Unit

No.	Residues
1	A:9	-	A:45
2	A:19	-	A:36
3	A:115	-	A:198
4	A:157	-	A:173
5	A:160	-	A:183
6	A:170	-	A:181
7	A:231	-	A:245
8	A:348	-	A:380
9	A:358	-	A:371
10	A:405	-	A:684
11	A:425	-	A:647
12	A:457	-	A:532
13	A:481	-	A:675
14	A:491	-	A:505
15	A:502	-	A:515
16	A:573	-	A:587
17	A:625	-	A:630

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

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

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.	TRFL_BUBBU	25-352 364-693	2	A:6-333 A:345-674
2	TRANSFERRIN_LIKE_1	PS00205	Transferrin-like domain signature 1.	TRFL_BUBBU	111-120 452-461	2	A:92-101 A:433-442
3	TRANSFERRIN_LIKE_2	PS00206	Transferrin-like domain signature 2.	TRFL_BUBBU	211-227 545-561	2	A:192-208 A:526-542
4	TRANSFERRIN_LIKE_3	PS00207	Transferrin-like domain signature 3.	TRFL_BUBBU	245-275 587-617	2	A:226-256 A:568-598

(no "Exon" information available for 1BIY)

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:689
 aligned with TRFL_BUBBU | O77698 from UniProtKB/Swiss-Prot  Length:708

    Alignment length:689
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699         
           TRFL_BUBBU    20 APRKNVRWCTISQPEWLKCHRWQWRMKKLGAPSITCVRRAFVLECIRAITEKKADAVTLDGGMVFEAGLDPYKLRPVAAEIYGTKESPQTHYYAVAVVKKGSNFQLDQLQGRNSCHTGLGRSAGWNIPMGILRPYLSWTESLEPFQGAVAKFFSASCVPCVDRQAYPNLCQLCKGEGENQCACSPREPYFGYSGAFKCLQDGAGDVAFVKETTVFENLPEKADRDQYELLCLNNTRAPVDAFKECHLAQVPSHAVVARSVDGKEDLIWKLLSKAQEKFGKNKSGSFQLFGSPPGQRDLLFKDCALGFLRIPSKVDSALYLGSRYLTALKNLRETAEEVQARRARVVWCAVGPEEQKKCQQWSQQSGQIVTCATASTTDDCIALVLKGEADALSLDGGYIYTAGKCGLVPVLAENRKSSKHSSLDCVLRPTEGYLAVAVVKKANEGLTWNSLKGKKSCHTAVDRTAGWNIPMGLIANQTGSCAFDEFFSQSCAPGADPKSRLCALCAGDDQGLDKCVPNSKEKYYGYTGAFRCLAEDVGDVAFVKNDTVWENTNGESTADWAKNLNREDFRLLCLDGTRKPVTEAQSCHLAVAPNHAVVSLSERAAHVEQVLLHQQALFGENGKNCPDKFCLFKSETKNLLFNDNTECLAKLGGRPTYEEYLGTEYVTAIANLKKCSTSPLLEACAFLTR 708
               SCOP domains d1biya1 A:1-333 Lactoferrin                                                                                                                                                                                                                                                                                                                  d1biya2 A:334-689 Lactoferrin                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ----1biyA01 A:5-91,A:251-339 Periplasmic binding protein-like II                           1biyA02 A:92-250 Periplasmic binding protein-like II                                                                                                           1biyA01 A:5-91,A:251-339 Periplasmic binding protein-like II                             1biyA03 A:340-432,A:595-689 Periplasmic binding protein-like II                              1biyA04 A:433-594 Periplasmic binding protein-like II                                                                                                             1biyA03 A:340-432,A:595-689 Periplasmic binding protein-like II                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee...hhhhhhhhhhhhhhh.......eee....hhhhhhhhh......eee.hhhhhhh......eeeeeee.eee..eee.eeeeeeeee.............eeee.........hhhhhhhhhhh........hhhhhhhh..eeee........hhhhhh....................hhhhhhhh.....eeeeehhhhhhh...hhhhhheeeee...eeeehhh......eeee..eeeee.....hhhhhhhhhhhhhhh............................eee......hhhh..hhhhhhhhhh...hhhhhhhhh.eeeeee.hhhhhhhhhhhhhh...eeeeee..hhhhhhhhhh....eeee.hhhhhhhhh.......eeee.........hhh.....eeeeeeee.......hhh....eeee...........hhhhhh.............eee.................................hhhhhhhhhh.....eeeeehhhhh...................eeee.....eeehhh......eee...eeee.hhhhhhhhhhhhhhhhhh..........................eeeee.......hhhhh.hhhhhhhhhhhhh...hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----TRANSFERRIN_LIKE_4  PDB: A:6-333 UniProt: 25-352                                                                                                                                                                                                                                                                                        -----------TRANSFERRIN_LIKE_4  PDB: A:345-674 UniProt: 364-693                                                                                                                                                                                                                                                                                       --------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------TRANSFERRI------------------------------------------------------------------------------------------TRANSFERRIN_LIKE_-----------------TRANSFERRIN_LIKE_3             --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRANSFERRI-----------------------------------------------------------------------------------TRANSFERRIN_LIKE_-------------------------TRANSFERRIN_LIKE_3             ------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1biy A   1 APRKNVRWCTISQPEWLKCHRWQWRMKKLGAPSITCVRRAFVLECIRAITEKKADAVTLDGGMVFEAGLDPYKLRPVAAEIYGTKESPQTHYYAVAVVKKGSNFQLDQLQGRNSCHTGLGRSAGWNIPMGILRPYLSWTESLEPLQGAVAKFFSASCVPCVDRQAYPNLCQLCKGEGENQCACSPREPYFGYSGAFKCLQDGAGDVAFVKETTVFENLPEKADRDQYELLCLNNTRAPVDAFKECHLAQVPSHAVVARSVDGKEDLIWKLLSKAQEKFGKNKSGSFQLFGSPPGQRDLLFKDSALGFLRIPSKVDSALYLGSRYLTALKNLRETAEEVQARRARVVWCAVGPEEQKKCQQWSQQSGQIVTCATASTTDDCIALVLKGEADALSLDGGYIYTAGKCGLVPVLAENRKSSKHSSLDCVLRPTEGYLAVAVVKKANEGLTWNSLKGKKSCHTAVDRTAGWNIPMGLIANQTGSCAFDEFFSQSCAPGADPKSRLCALCAGDDQGLDKCVPNSKEKYYGYTGAFRCLAEDVGDVAFVKNDTVWENTNGESTADWAKNLNREDFRLLCLDGTRKPVTEAQSCHLAVAPNHAVVSLSERAAHVEQVLLHQQALFGENGKNCPDKFCLFKSETKNLLFNDNTECLAKLGGRPTYEEYLGTEYVTAIANLKKCSTSPLLEACAFLTR 689
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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: Lactoferrin (42)

Domestic water buffalo (Bubalus arnee bubalis) [TaxId: 89462] (2)

1a	d1biya1	A:1-333
1b	d1biya2	A:334-689

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)

Water buffalo (Bubalus bubalis) (2)

1a	1biyA02	A:92-250
1b	1biyA04	A:433-594
1c	1biyA01	A:5-91,A:251-339
1d	1biyA03	A:340-432,A:595-689

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TRFL_BUBBU | O77698)

molecular function
	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:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0008236	serine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
	GO:0019731	antibacterial humoral response	An immune response against bacteria mediated through a body fluid. Examples of this process are the antibacterial humoral responses in Mus musculus and Drosophila melanogaster.
	GO:0019732	antifungal humoral response	An immune response against a fungus mediated through a body fluid. An example of this process is the antifungal humoral response in Drosophila melanogaster.
	GO:0060349	bone morphogenesis	The process in which bones are generated and organized.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0002227	innate immune response in mucosa	Any process of the innate immune response that takes place in the mucosal tissues.
	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:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:0031665	negative regulation of lipopolysaccharide-mediated signaling pathway	Any process that stops, prevents, or reduces the frequency, rate or extent of signaling in response to detection of lipopolysaccharide.
	GO:2001205	negative regulation of osteoclast development	Any process that stops, prevents or reduces the frequency, rate or extent of osteoclast development.
	GO:1900229	negative regulation of single-species biofilm formation in or on host organism	Any process that stops, prevents or reduces the frequency, rate or extent of single-species biofilm formation in or on host organism.
	GO:2000308	negative regulation of tumor necrosis factor (ligand) superfamily member 11 production	Any process that stops, prevents or reduces the frequency, rate or extent of tumor necrosis factor (ligand) superfamily member 11 production.
	GO:0001503	ossification	The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
	GO:1900159	positive regulation of bone mineralization involved in bone maturation	Any process that activates or increases the frequency, rate or extent of bone mineralization involved in bone maturation.
	GO:1902732	positive regulation of chondrocyte proliferation	Any process that increases the frequency, rate or extent of the multiplication or reproduction of chondrocytes by cell division, resulting in the expansion of their population. A chondrocyte is a polymorphic cell that forms cartilage.
	GO:0045669	positive regulation of osteoblast differentiation	Any process that activates or increases the frequency, rate or extent of osteoblast differentiation.
	GO:0033690	positive regulation of osteoblast proliferation	Any process that activates or increases the rate or extent of osteoblast proliferation.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0001817	regulation of cytokine production	Any process that modulates the frequency, rate, or extent of production of a cytokine.
	GO:0032680	regulation of tumor necrosis factor production	Any process that modulates the frequency, rate, or extent of tumor necrosis factor production.
	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.
	GO:0042581	specific granule	Granule with a membranous, tubular internal structure, found primarily in mature neutrophil cells. Most are released into the extracellular fluid. Specific granules contain lactoferrin, lysozyme, vitamin B12 binding protein and elastase.

Asymmetric/Biological Unit
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Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (6, 6)

SS Bonds (17, 17)

Cis Peptide Bonds (0, 0)

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