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(-) Description

Title :  CRYSTAL STRUCTURE OF BPI, THE HUMAN BACTERICIDAL PERMEABILITY-INCREASING PROTEIN
 
Authors :  L. J. Beamer, S. F. Carroll, D. Eisenberg
Date :  08 Apr 97  (Deposition) - 04 Sep 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Bactericidal, Permeability-Increasing, Lipid-Binding, Lipopolysaccharide-Binding, Antibiotic (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. J. Beamer, S. F. Carroll, D. Eisenberg
Crystal Structure Of Human Bpi And Two Bound Phospholipids At 2. 4 Angstrom Resolution.
Science V. 276 1861 1997
PubMed-ID: 9188532  |  Reference-DOI: 10.1126/SCIENCE.276.5320.1861
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BACTERICIDAL/PERMEABILITY-INCREASING PROTEIN
    CellPOLYMORPHONUCLEAR NEUTROPHILS
    ChainsA
    EngineeredYES
    Expression SystemCRICETULUS GRISEUS
    Expression System Cellular LocationPRIMARY GRANULES
    Expression System Cell LineCHINESE HAMSTER OVARY CELLS (CHO)
    Expression System CommonCHINESE HAMSTER
    Expression System Taxid10029
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBPI

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1PC12Ligand/Ion1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:7 , ILE A:9 , ALA A:17 , GLN A:20 , GLY A:21 , ALA A:24 , ILE A:68 , SER A:181 , LYS A:185 , LEU A:186 , TYR A:189 , PHE A:190 , LEU A:193 , VAL A:254 , PRO A:428 , PRO A:430 , ARG A:432 , TYR A:455BINDING SITE FOR RESIDUE PC1 A 777
2AC2SOFTWARESER A:201 , PHE A:263 , ALA A:266 , TYR A:270 , LEU A:276 , PRO A:324 , PHE A:335 , PRO A:337 , THR A:362 , VAL A:368 , LEU A:375 , VAL A:417 , LYS A:420 , PHE A:425BINDING SITE FOR RESIDUE PC1 A 778
3CUNKNOWNLYS A:456APOLAR POCKET PRIMARILY IN C-TERMINAL DOMAIN OF PROTEIN WHICH HOLDS ONE PHOSPHATIDYLCHOLINE MOLECULE.
4NUNKNOWNVAL A:1APOLAR POCKET PRIMARILY IN N-TERMINAL DOMAIN OF PROTEIN WHICH HOLDS ONE PHOSPHATIDYLCHOLINE MOLECULE.

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:135 -A:175

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:303 -Glu A:304

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (8, 8)

Asymmetric/Biological Unit (8, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_049730R90CBPI_HUMANPolymorphism5743500AR59C
2UniProtVAR_049732E140QBPI_HUMANPolymorphism5743506AE109Q
3UniProtVAR_018402A196VBPI_HUMANPolymorphism5743509AA165V
4UniProtVAR_018403E216KBPI_HUMANPolymorphism4358188AK185K
5UniProtVAR_049733A280VBPI_HUMANPolymorphism5741804AA249V
6UniProtVAR_049734V377IBPI_HUMANPolymorphism5743524AV346I
7UniProtVAR_049735N404DBPI_HUMANPolymorphism5741809AN373D
8UniProtVAR_049736K451EBPI_HUMANPolymorphism5743542AK420E

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LBP_BPI_CETPPS00400 LBP / BPI / CETP family signature.BPI_HUMAN34-66  1A:3-35

(-) Exons   (15, 15)

Asymmetric/Biological Unit (15, 15)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.5aENST000002628655aENSE00000800529chr20:36932525-36932755231BPI_HUMAN1-48481A:1-1717
1.6ENST000002628656ENSE00000661935chr20:36935969-36936083115BPI_HUMAN48-86391A:17-5539
1.7ENST000002628657ENSE00000661936chr20:36937332-36937460129BPI_HUMAN86-129441A:55-9844
1.8ENST000002628658ENSE00000661937chr20:36938893-36939054162BPI_HUMAN129-183551A:98-15255
1.9ENST000002628659ENSE00000661938chr20:36940276-3694033964BPI_HUMAN183-204221A:152-17322
1.11ENST0000026286511ENSE00000906853chr20:36946815-3694687864BPI_HUMAN205-226221A:174-19522
1.13bENST0000026286513bENSE00000906854chr20:36948585-3694867692BPI_HUMAN226-256311A:195-22531
1.15aENST0000026286515aENSE00000906855chr20:36952272-36952448177BPI_HUMAN257-315591A:226-28459
1.16ENST0000026286516ENSE00000906856chr20:36953176-3695323560BPI_HUMAN316-335201A:285-30420
1.17ENST0000026286517ENSE00000906857chr20:36954667-36954834168BPI_HUMAN336-391561A:305-36056
1.18ENST0000026286518ENSE00000906858chr20:36955990-3695605768BPI_HUMAN392-414231A:361-38323
1.19ENST0000026286519ENSE00000844627chr20:36959450-3695949243BPI_HUMAN414-428151A:383-39715
1.20ENST0000026286520ENSE00000844628chr20:36962832-3696289564BPI_HUMAN429-450221A:398-41922
1.21cENST0000026286521cENSE00000844629chr20:36964000-3696407677BPI_HUMAN450-475261A:419-44426
1.22cENST0000026286522cENSE00001944087chr20:36965548-36965907360BPI_HUMAN476-487121A:445-45612

(-) 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:456
 aligned with BPI_HUMAN | P17213 from UniProtKB/Swiss-Prot  Length:487

    Alignment length:456
                                    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      
            BPI_HUMAN    32 VNPGVVVRISQKGLDYASQQGTAALQKELKRIKIPDYSDSFKIKHLGKGHYSFYSMDIREFQLPSSQISMVPNVGLKFSISNANIKISGKWKAQKRFLKMSGNFDLSIEGMSISADLKLGSNPTSGKPTITCSSCSSHINSVHVHISKSKVGWLIQLFHKKIESALRNKMNSQVCEKVTNSVSSELQPYFQTLPVMTKIDSVAGINYGLVAPPATTAETLDVQMKGEFYSENHHNPPPFAPPVMEFPAAHDRMVYLGLSDYFFNTAGLVYQEAGVLKMTLRDDMIPKESKFRLTTKFFGTFLPEVAKKFPNMKIQIHVSASTPPHLSVQPTGLTFYPAVDVQAFAVLPNSSLASLFLIGMHTTGSMEVSAESNRLVGELKLDRLLLELKHSNIGPFPVELLQDIMNYIVPILVLPRVNEKLQKGFPLPTPARVQLYNVVLQPHQNFLLFGADVVYK 487
               SCOP domains d1bp1a1 A:1-217 Bactericidal permeability-increasing protein, BPI                                                                                                                                                        d1bp1a2 A:218-456 Bactericidal permeability-increasing protein, BPI                                                                                                                                                                             SCOP domains
               CATH domains 1bp1A02    1bp1A01 A:12-191 Bactericidal permeability-increasing protein; domain 1                                                                                                             1bp1A02 A:1-11,A:192-456 Bactericidal permeability-increasing protein; domain 2                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeehhhhhhhhhhhhhhhhhhhhh.....eeeeeee...eeeeeeee..eeeeee...eeeeee...eeeeee...eeeeeeeeeeee..eeeeeeeeeeee...eeeeeeeeee....eeeeeeeeee....eeeee......hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.hhhhh.....eee....eeee............eeeeee..eeee.......................eeeeeehhhhhhhhhhhhh....eeee..............hhhhhhhh..hhhh.....eeeeeee....eeeee..eeeee.eeeeeeeee.....eeeeeeeeee..eeeeeeee..eeeeeeee......eeee......hhhhhhhhhhhhhhhhhhhhhhhhhh.........eeee..eeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------C-------------------------------------------------Q-------------------------------------------------------V-------------------K---------------------------------------------------------------V------------------------------------------------------------------------------------------------I--------------------------D----------------------------------------------E------------------------------------ SAPs(SNPs)
                    PROSITE --LBP_BPI_CETP  PDB: A:3-35        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5a        -------------------------------------Exon 1.7  PDB: A:55-98 UniProt: 86-129      -----------------------------------------------------Exon 1.9              Exon 1.11             ------------------------------Exon 1.15a  PDB: A:226-284 UniProt: 257-315                Exon 1.16           Exon 1.17  PDB: A:305-360 UniProt: 336-391              Exon 1.18              --------------Exon 1.20             -------------------------Exon 1.22c   Transcript 1 (1)
           Transcript 1 (2) ----------------Exon 1.6  PDB: A:17-55 UniProt: 48-86  ------------------------------------------Exon 1.8  PDB: A:98-152 UniProt: 129-183               ------------------------------------------Exon 1.13b  PDB: A:195-225     -------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.19      ---------------------Exon 1.21c  PDB: A:419-444------------ Transcript 1 (2)
                 1bp1 A   1 VNPGVVVRISQKGLDYASQQGTAALQKELKRIKIPDYSDSFKIKHLGKGHYSFYSMDIREFQLPSSQISMVPNVGLKFSISNANIKISGKWKAQKRFLKMSGNFDLSIEGMSISADLKLGSNPTSGKPTITCSSCSSHINSVHVHISKSKVGWLIQLFHKKIESALRNKMNSQVCEKVTNSVSSKLQPYFQTLPVMTKIDSVAGINYGLVAPPATTAETLDVQMKGEFYSENHHNPPPFAPPVMEFPAAHDRMVYLGLSDYFFNTAGLVYQEAGVLKMTLRDDMIPKESKFRLTTKFFGTFLPEVAKKFPNMKIQIHVSASTPPHLSVQPTGLTFYPAVDVQAFAVLPNSALASLFLIGMHTTGSMEVSAESNRLVGELKLDRLLLELKHSNIGPFPVELLQDIMNYIVPILVLPRVNEKLQKGFPLPTPARVQLYNVVLQPHQNFLLFGADVVYK 456
                                    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      

   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  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BP1)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (BPI_HUMAN | P17213)
molecular function
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0001530    lipopolysaccharide binding    Interacting selectively and non-covalently with lipopolysaccharide.
biological process
    GO:0050829    defense response to Gram-negative bacterium    Reactions triggered in response to the presence of a Gram-negative bacterium that act to protect the cell or organism.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0032715    negative regulation of interleukin-6 production    Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-6 production.
    GO:0032717    negative regulation of interleukin-8 production    Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-8 production.
    GO:0043031    negative regulation of macrophage activation    Any process that stops, prevents, or reduces the frequency, rate or extent of macrophage activation.
    GO:0032720    negative regulation of tumor necrosis factor production    Any process that stops, prevents, or reduces the frequency, rate, or extent of tumor necrosis factor production.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        BPI_HUMAN | P172131ewf

(-) Related Entries Specified in the PDB File

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