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(-) Description

Title :  STRUCTURE OF EQUINE APOLACTOFERRIN AT 3.2 A RESOLUTION USING CRYSTALS GROWN AT 303K
 
Authors :  P. Kumar, S. Yadav, T. P. Singh
Date :  02 Mar 01  (Deposition) - 13 Feb 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Lactoferrin, Equine, Structure, Apo, Transferrin, Crystal, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Kumar, J. A. Khan, S. Yadav, T. P. Singh
Crystal Structure Of Equine Apolactoferrin At 303 K Providing Further Evidence Of Closed Conformations Of N And C Lobes.
Acta Crystallogr. , Sect. D V. 58 225 2002
PubMed-ID: 11807246  |  Reference-DOI: 10.1107/S090744490101993X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LACTOTRANSFERRIN
    ChainsA
    Organism CommonHORSE
    Organism ScientificEQUUS CABALLUS
    Organism Taxid9796
    SynonymLACTOFERRIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1I6B)

(-) Sites  (0, 0)

(no "Site" information available for 1I6B)

(-) SS Bonds  (17, 17)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1I6B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1I6B)

(-) PROSITE Motifs  (4, 8)

Asymmetric/Biological Unit (4, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRANSFERRIN_LIKE_4PS51408 Transferrin-like domain profile.TRFL_HORSE12-339
351-680
  2A:6-333
A:345-674
2TRANSFERRIN_LIKE_1PS00205 Transferrin-like domain signature 1.TRFL_HORSE98-107
439-448
  2A:92-101
A:433-442
3TRANSFERRIN_LIKE_2PS00206 Transferrin-like domain signature 2.TRFL_HORSE198-214
532-548
  2A:192-208
A:526-542
4TRANSFERRIN_LIKE_3PS00207 Transferrin-like domain signature 3.TRFL_HORSE232-262
574-604
  2A:226-256
A:568-598

(-) Exons   (0, 0)

(no "Exon" information available for 1I6B)

(-) Sequences/Alignments

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_HORSE | O77811 from UniProtKB/Swiss-Prot  Length:695

    Alignment length:689
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686         
           TRFL_HORSE     7 APRKSVRWCTISPAEAAKCAKFQRNMKKVRGPSVSCIRKTSSFECIQAIAANKADAVTLDGGLVYEAGLHPYKLRPVAAEVYQTRGKPQTRYYAVAVVKKGSGFQLNQLQGVKSCHTGLGRSAGWNIPIGTLRPYLNWTGPPEPLQKAVANFFSASCVPCADGKQYPNLCRLCAGTEADKCACSSQEPYFGYSGAFKCLENGAGDVAFVKDSTVFENLPDEADRDKYELLCPDNTRKPVDAFKECHLARVPSHAVVARSVDGREDLIWRLLHRAQEEFGRNKSSAFQLFKSTPENKDLLFKDSALGFVRIPSQIDSGLYLGANYLTATQNLRETAAEVAARRERVVWCAVGPEEERKCKQWSDVSNRKVACASASTTEECIALVLKGEADALNLDGGFIYVAGKCGLVPVLAENQKSQNSNAPDCVHRPPEGYLAVAVVRKSDADLTWNSLSGKKSCHTGVGRTAAWNIPMGLLFNQTGSCKFDKFFSQSCAPGADPQSSLCALCVGNNENENKCMPNSEERYYGYTGAFRCLAEKAGDVAFVKDVTVLQNTDGKNSEPWAKDLKQEDFELLCLDGTRKPVAEAESCHLARAPNHAVVSQSDRAQHLKKVLFLQQDQFGGNGPDCPGKFCLFKSETKNLLFNDNTECLAELQGKTTYEQYLGSEYVTSITNLRRCSSSPLLEACAFLRA 695
               SCOP domains d1i6ba1 A:1-333 Lactoferrin                                                                                                                                                                                                                                                                                                                  d1i6ba2 A:334-689 Lactoferrin                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1i6bA01 A:1-91,A:251-339 Periplasmic binding protein-like II                               1i6bA02 A:92-250 Periplasmic binding protein-like II                                                                                                           1i6bA01 A:1-91,A:251-339 Periplasmic binding protein-like II                             1i6bA03 A:340-432,A:593-689 Periplasmic binding protein-like II                              1i6bA04 A:433-592 Periplasmic binding protein-like II                                                                                                           1i6bA03 A:340-432,A:593-689 Periplasmic binding protein-like II                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhh..........hhhhhhhhhh.......eehhhhhhhhh.....eeeeeeee.........eeee.eeee.....hhhhhh...eee........hhhhhhhhh..........hhhhhhhh...............hhhhh..................hhhhhhhhhhhh....eee...hhhhhhh.hhhhhh.eeeee...eee..........eeee..eeeee....hhhhhhhhhhhhhhhh...........................eeee.....hhhhhhhhhhhhh......hhhhhhhhhh.eeeeeehhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh...eeeehhhhhhhhhhh..eeeeeee........hhhhh.....eeeeee................eee.........hhhhhhhhhhhh...hhhhhh.eee..................................hhhhhhhhh......eeeehhhhhh...................ee.......ee.........eee...eeee...hhhhhhhhhhhhhhhh............................eee......hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----TRANSFERRIN_LIKE_4  PDB: A:6-333 UniProt: 12-339                                                                                                                                                                                                                                                                                        -----------TRANSFERRIN_LIKE_4  PDB: A:345-674 UniProt: 351-680                                                                                                                                                                                                                                                                                       --------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------TRANSFERRI------------------------------------------------------------------------------------------TRANSFERRIN_LIKE_-----------------TRANSFERRIN_LIKE_3             --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRANSFERRI-----------------------------------------------------------------------------------TRANSFERRIN_LIKE_-------------------------TRANSFERRIN_LIKE_3             ------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i6b A   1 APRKSVRWCTISPAEAAKCAKFQRNMKKVRGPSVSCIRKTSSFECIQAIAANKADAVTLDGGLVYEAGLHPYKLRPVAAEVYQTRGKPQTRYYAVAVVKKGSGFQLNQLQGVKSCHTGLGRSAGWNIPIGTLRPYLNWTGPPEPLQKAVANFFSASCVPCADGKQYPNLCRLCAGTEADKCACSSQEPYFGYSGAFKCLENGAGDVAFVKDSTVFENLPDEAERDKYELLCPDNTRKPVDAFKECHLARVPSHAVVARSVDGREDLIWKLLHRAQEEFGRNKSSAFQLFGSTPGEQDLLFKDSALGFVRIPSQIDSGLYLGANYLTATQNLRETAAEVAARRERVVWCAVGPEEERKCKQWSDVSNRKVACASASTTEECIALVLKGEADALNLDGGFIYVAGKCGLVPVLAENQKSQNSNAPDCVHRPPEGYLAVAVVRKSDADLTWNSLSGKKSCHTGVGRTAAWNIPMGLLFNQTGSCKFDKFFSQSCAPGADPQSSLCALCVGNNENENKCMPNSEERYYGYTGAFRCLAEKAGDVAFVKDVTVLQNTDGKNSEPWAKDLKQEDFELLCLDGTRKPVAEAESCHLARAPNHAVVSQSDRAQHLKKVLFLQQDQFGGNGPDCPGKFCLFKSETKNLLFNDNTECLAELQGKTTYEQYLGSEYVTSITNLRRCSSSPLLEACAFLRA 689
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680         

   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1I6B)

(-) Gene Ontology  (28, 28)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TRFL_HORSE | O77811)
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: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: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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        TRFL_HORSE | O778111b1x 1b7u 1b7z 1f9b 1qjm 3cr9

(-) Related Entries Specified in the PDB File

1i6q FORMATION OF A PROTEIN INTERMEDIATE AND ITS TRAPPING BY THE SIMULTANEOUS CRYSTALLIZATION PROCESS: CRYSTAL STRUCTURE OF AN IRON-SATURATED INTERMEDIATE IN THE FE3+ BINDING PATHWAY OF CAMEL LACTOFERRIN AT 2.7 RESOLUTION