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(-) Description

Title :  CRYSTAL STRUCTURE OF CHOLESTERYL ESTER TRANSFER PROTEIN
 
Authors :  X. Qiu
Date :  18 Dec 06  (Deposition) - 23 Jan 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Cholesteryl Ester, Lipid Transfer Protein, Lipid Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Qiu, A. Mistry, M. J. Ammirati, B. A. Chrunyk, R. W. Clark, Y. Cong, J. S. Culp, D. E. Danley, T. B. Freeman, K. F. Geoghegan, M. C. Griffor, S. J. Hawrylik, C. M. Hayward, P. Hensley, L. R. Hoth, G. A. Karam, M. E. Lira, D. B. Lloyd, K. M. Mcgrath, K. J. Stutzman-Engwall, A. K. Subashi, T. A. Subashi, J. F. Thompson, I. K. Wang, H. Zhao, A. P. Seddon
Crystal Structure Of Cholesteryl Ester Transfer Protein Reveals A Long Tunnel And Four Bound Lipid Molecules.
Nat. Struct. Mol. Biol. V. 14 106 2007
PubMed-ID: 17237796  |  Reference-DOI: 10.1038/NSMB1197
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CHOLESTERYL ESTER TRANSFER PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemCRICETULUS GRISEUS
    Expression System Cell LineCHINESE HAMSTER OVARY DG44
    Expression System CommonCHINESE HAMSTER
    Expression System Taxid10029
    GeneCETP
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymLIPID TRANSFER PROTEIN I

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 12)

Asymmetric/Biological Unit (8, 12)
No.NameCountTypeFull Name
11PE2Ligand/IonPENTAETHYLENE GLYCOL
22OB2Ligand/IonCHOLESTERYL OLEATE
3CL1Ligand/IonCHLORIDE ION
4EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
5FU41Ligand/Ion2,6-ANHYDRO-1-DEOXY-D-GALACTITOL
6NDG2Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
7PCW2Ligand/Ion1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
8PG41Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:399 , NDG A:482BINDING SITE FOR RESIDUE NDG A 481
02AC2SOFTWAREASN A:396 , LEU A:397 , THR A:398 , GLU A:399 , SER A:401 , NDG A:481 , FU4 A:483BINDING SITE FOR RESIDUE NDG A 482
03AC3SOFTWARESER A:401 , SER A:402 , GLU A:403 , NDG A:482 , HOH A:498 , HOH A:634BINDING SITE FOR RESIDUE FU4 A 483
04AC4SOFTWAREARG A:158 , GLN A:388 , ILE A:389BINDING SITE FOR RESIDUE CL A 493
05AC5SOFTWAREILE A:15 , VAL A:136 , VAL A:198 , GLN A:199 , ALA A:202 , LEU A:228 , SER A:230 , HIS A:232 , LEU A:261 , PHE A:263 , PHE A:441 , PHE A:461BINDING SITE FOR RESIDUE 2OB A 485
06AC6SOFTWAREPHE A:292 , VAL A:321 , VAL A:323 , VAL A:340 , ILE A:367 , THR A:369 , TYR A:375 , VAL A:416 , GLY A:417 , VAL A:421 , MET A:422 , LEU A:425 , LEU A:457 , PCW A:488BINDING SITE FOR RESIDUE 2OB A 486
07AC7SOFTWARELEU A:23 , THR A:27 , VAL A:74 , PHE A:197 , ARG A:201 , SER A:435 , GLY A:437 , PHE A:441 , LEU A:467 , HOH A:870BINDING SITE FOR RESIDUE PCW A 487
08AC8SOFTWARELEU A:206 , ASP A:208 , PHE A:265 , LEU A:273 , GLY A:281 , ARG A:282 , LEU A:283 , MET A:284 , CYS A:325 , ILE A:331 , SER A:342 , ARG A:424 , LEU A:425 , VAL A:428 , PHE A:429 , 2OB A:486 , HOH A:607 , HOH A:757BINDING SITE FOR RESIDUE PCW A 488
09AC9SOFTWAREASP A:114 , GLY A:314 , PHE A:315 , PRO A:316 , SER A:317BINDING SITE FOR RESIDUE EPE A 489
10BC1SOFTWAREHIS A:60 , LYS A:98 , SER A:112BINDING SITE FOR RESIDUE 1PE A 490
11BC2SOFTWARETRP A:106 , THR A:298 , LEU A:384 , HOH A:590 , HOH A:741 , HOH A:771BINDING SITE FOR RESIDUE 1PE A 491
12BC3SOFTWAREALA A:131 , LEU A:217 , THR A:218 , GLY A:219 , ASP A:220 , HOH A:784 , HOH A:817BINDING SITE FOR RESIDUE PG4 A 492

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:143 -A:184

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Val A:312 -Gly A:313

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (11, 11)

Asymmetric/Biological Unit (11, 11)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_033098R154WCETP_HUMANPolymorphism34716057AR137W
02UniProtVAR_033099L168PCETP_HUMANDisease (HALP1)  ---AL151P
03UniProtVAR_033100R299CCETP_HUMANDisease (HALP1)142459781AR282C
04UniProtVAR_013919G331SCETP_HUMANPolymorphism5881AG314S
05UniProtVAR_017019V385MCETP_HUMANPolymorphism34855278AV368M
06UniProtVAR_013920A390PCETP_HUMANPolymorphism5880AA373P
07UniProtVAR_013921V422ICETP_HUMANPolymorphism5882AI405I
08UniProtVAR_031127V455MCETP_HUMANPolymorphism2228667AV438M
09UniProtVAR_004172D459GCETP_HUMANDisease (HALP1)2303790AD442G
10UniProtVAR_013922R468QCETP_HUMANPolymorphism1800777AR451Q
11UniProtVAR_013923V486MCETP_HUMANPolymorphism5887AV469M

  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.CETP_HUMAN26-58  1A:9-41

(-) Exons   (16, 16)

Asymmetric/Biological Unit (16, 16)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002006761aENSE00001820497chr16:56995762-56996009248CETP_HUMAN1-40401A:5-2319
1.2ENST000002006762ENSE00001108758chr16:56996922-56997036115CETP_HUMAN40-78391A:23-6139
1.3ENST000002006763ENSE00000685107chr16:57003298-57003432135CETP_HUMAN78-123461A:61-10646
1.4ENST000002006764ENSE00000685106chr16:57003523-5700359371CETP_HUMAN123-147251A:106-13025
1.5ENST000002006765ENSE00000685105chr16:57003826-5700391388CETP_HUMAN147-176301A:130-15930
1.6ENST000002006766ENSE00000685103chr16:57004945-5700501470CETP_HUMAN176-199241A:159-18224
1.7ENST000002006767ENSE00000685102chr16:57005233-5700529361CETP_HUMAN200-220211A:183-20321
1.8ENST000002006768ENSE00000685101chr16:57005904-5700599592CETP_HUMAN220-250311A:203-23331
1.9ENST000002006769ENSE00000685100chr16:57007243-57007422180CETP_HUMAN251-310601A:234-29360
1.10ENST0000020067610ENSE00000685099chr16:57009013-5700906351CETP_HUMAN311-327171A:294-31017
1.11ENST0000020067611ENSE00000685096chr16:57012003-57012167165CETP_HUMAN328-382551A:311-36555
1.12ENST0000020067612ENSE00000685095chr16:57015070-5701513768CETP_HUMAN383-405231A:366-38823
1.13ENST0000020067613ENSE00000685094chr16:57015559-5701559234CETP_HUMAN405-416121A:388-39912
1.14ENST0000020067614ENSE00000685093chr16:57016077-5701614973CETP_HUMAN417-441251A:400-42425
1.15ENST0000020067615ENSE00000685092chr16:57017238-5701732386CETP_HUMAN441-469291A:424-45229
1.16bENST0000020067616bENSE00001925693chr16:57017504-57017757254CETP_HUMAN470-493241A:453-47624

(-) 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:472
 aligned with CETP_HUMAN | P11597 from UniProtKB/Swiss-Prot  Length:493

    Alignment length:472
                                    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  
           CETP_HUMAN    22 TSHEAGIVCRITKPALLVLNHETAKVIQTAFQRASYPDITGEKAMMLLGQVKYGLHNIQISHLSIASSQVELVEAKSIDVSIQNVSVVFKGTLKYGYTTAWWLGIDQSIDFEIDSAIDLQINTQLTCDSGRVRTDAPDCYLSFHKLLLHLQGEREPGWIKQLFTNFISFTLKLVLKGQICKEINVISNIMADFVQTRAASILSDGDIGVDISLTGDPVITASYLESHHKGHFIYKNVSEDLPLPTFSPTLLGDSRMLYFWFSERVFHSLAKVAFQDGRLMLSLMGDEFKAVLETWGFNTNQEIFQEVVGGFPSQAQVTVHCLKMPKISCQNKGVVVNSSVMVKFLFPRPDQQHSVAYTFEEDIVTTVQASYSKKKLFLSLLDFQITPKTVSNLTESSSESVQSFLQSMITAVGIPEVMSRLEVVFTALMNSKGVSLFDIINPEIITRDGFLLLQMDFGFPEHLLVDFLQSLS 493
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------LBP_BPI_CETP-2obdA01 A:19-199                                                                                                                                                        --------------------------LBP_BPI_CETP_C-2obdA02 A:226-463                                                                                                                                                                                                              ------------- Pfam domains
         Sec.struct. author ..ee..eeeeeehhhhhhhh.hhhhhhhhhhhhh....eeeeeee...eeeeeeeeeeeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeeeee..hhhhh..eeeeeeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee.......ee...eeeeee..eeee..........eehhhhh.....eeeeeehhhhhhhhhhhhhh...eeeehhhhhhhhhhhh.....hhhhhhhhh.hhhhheeeeee....eeeee..eeeeeeeeeeeee....hhhhh..eeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeeeee..eeeeeeeee.hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------W-------------P----------------------------------------------------------------------------------------------------------------------------------C-------------------------------S-----------------------------------------------------M----P-------------------------------I--------------------------------M---G--------Q-----------------M------- SAPs(SNPs)
                    PROSITE ----LBP_BPI_CETP  PDB: A:9-41        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a          -------------------------------------Exon 1.3  PDB: A:61-106 UniProt: 78-123       -----------------------Exon 1.5  PDB: A:130-159      -----------------------Exon 1.7             ------------------------------Exon 1.9  PDB: A:234-293 UniProt: 251-310                   Exon 1.10        Exon 1.11  PDB: A:311-365 UniProt: 328-382             Exon 1.12              -----------Exon 1.14  PDB: A:400-424----------------------------Exon 1.16b               Transcript 1 (1)
           Transcript 1 (2) ------------------Exon 1.2  PDB: A:23-61 UniProt: 40-78  --------------------------------------------Exon 1.4  PDB: A:106-130 ----------------------------Exon 1.6  PDB: A:159-182--------------------Exon 1.8  PDB: A:203-233       ----------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.13   ------------------------Exon 1.15  PDB: A:424-452    ------------------------ Transcript 1 (2)
                 2obd A   5 TSHEAGIVCRITKPALLVLNHETAKVIQTAFQRASYPDITGEKAMMLLGQVKYGLHNIQISHLSIASSQVELVEAKSIDVSIQDVSVVFKGTLKYGYTTAWWLGIDQSIDFEIDSAIDLQINTQLTADSGRVRTDAPDCYLSFHKLLLHLQGEREPGWIKQLFTNFISFTLKLVLKGQICKEINVISNIMADFVQTRAASILSDGDIGVDISLTGDPVITASYLESHHKGHFIYKDVSEDLPLPTFSPTLLGDSRMLYFWFSERVFHSLAKVAFQDGRLMLSLMGDEFKAVLETWGFNTNQEIFQEVVGGFPSQAQVTVHCLKMPKISCQNKGVVVDSSVMVKFLFPRPDQQHSVAYTFEEDIVTTVQASYSKKKLFLSLLDFQITPKTVSNLTESSSESIQSFLQSMITAVGIPEVMSRLEVVFTALMNSKGVSLFDIINPEIITRDGFLLLQMDFGFPEHLLVDFLQSLS 476
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474  

   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  (0, 0)

(no "SCOP Domain" information available for 2OBD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2OBD)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (34, 34)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CETP_HUMAN | P11597)
molecular function
    GO:0015485    cholesterol binding    Interacting selectively and non-covalently with cholesterol (cholest-5-en-3-beta-ol); the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones.
    GO:0017127    cholesterol transporter activity    Enables the directed movement of cholesterol into, out of or within a cell, or between cells. Cholesterol is the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0005319    lipid transporter activity    Enables the directed movement of lipids into, out of or within a cell, or between cells.
    GO:0031210    phosphatidylcholine binding    Interacting selectively and non-covalently with phosphatidylcholine, a class of glycophospholipids in which a phosphatidyl group is esterified to the hydroxyl group of choline.
    GO:0005548    phospholipid transporter activity    Enables the directed movement of phospholipids into, out of or within a cell, or between cells. Phospholipids are a class of lipids containing phosphoric acid as a mono- or diester.
    GO:0017129    triglyceride binding    Interacting selectively and non-covalently with any triester of glycerol.
biological process
    GO:0042632    cholesterol homeostasis    Any process involved in the maintenance of an internal steady state of cholesterol within an organism or cell.
    GO:0008203    cholesterol metabolic process    The chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. It is a component of the plasma membrane lipid bilayer and of plasma lipoproteins and can be found in all animal tissues.
    GO:0030301    cholesterol transport    The directed movement of cholesterol, cholest-5-en-3-beta-ol, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0034375    high-density lipoprotein particle remodeling    The acquisition, loss or modification of a protein or lipid within a high-density lipoprotein particle, including the hydrolysis of triglyceride by hepatic lipase, with the subsequent loss of free fatty acid, and the transfer of cholesterol esters from LDL to a triglyceride-rich lipoprotein particle by cholesteryl ester transfer protein (CETP), with the simultaneous transfer of triglyceride to LDL.
    GO:0055088    lipid homeostasis    Any process involved in the maintenance of an internal steady state of lipid within an organism or cell.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0006869    lipid transport    The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0042157    lipoprotein metabolic process    The chemical reactions and pathways involving any conjugated, water-soluble protein in which the covalently attached nonprotein group consists of a lipid or lipids.
    GO:0034374    low-density lipoprotein particle remodeling    The acquisition, loss or modification of a protein or lipid within a low-density lipoprotein particle, including the hydrolysis of triglyceride by hepatic lipase, with the subsequent loss of free fatty acid, and the transfer of cholesterol esters from LDL to a triglyceride-rich lipoprotein particle by cholesteryl ester transfer protein (CETP), with the simultaneous transfer of triglyceride to LDL.
    GO:0010745    negative regulation of macrophage derived foam cell differentiation    Any process that decreases the rate, frequency or extent of macrophage derived foam cell differentiation. Macrophage derived foam cell differentiation is the process in which a macrophage acquires the specialized features of a foam cell. A foam cell is a type of cell containing lipids in small vacuoles and typically seen in atherosclerotic lesions, as well as other conditions.
    GO:0046470    phosphatidylcholine metabolic process    The chemical reactions and pathways involving phosphatidylcholines, any of a class of glycerophospholipids in which the phosphatidyl group is esterified to the hydroxyl group of choline. They are important constituents of cell membranes.
    GO:0055091    phospholipid homeostasis    Any process involved in the maintenance of an internal steady state of phospholipid within an organism or cell.
    GO:0015914    phospholipid transport    The directed movement of phospholipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Phospholipids are any lipids containing phosphoric acid as a mono- or diester.
    GO:0006898    receptor-mediated endocytosis    An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
    GO:0010874    regulation of cholesterol efflux    Any process that modulates the frequency, rate or extent of cholesterol efflux. Cholesterol efflux is the directed movement of cholesterol, cholest-5-en-3-beta-ol, out of a cell or organelle.
    GO:0043691    reverse cholesterol transport    The directed movement of peripheral cell cholesterol, cholest-5-en-3-beta-ol, towards the liver for catabolism.
    GO:0008202    steroid metabolic process    The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
    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.
    GO:0070328    triglyceride homeostasis    Any process involved in the maintenance of an internal steady state of triglyceride within an organism or cell.
    GO:0006641    triglyceride metabolic process    The chemical reactions and pathways involving triglyceride, any triester of glycerol. The three fatty acid residues may all be the same or differ in any permutation. Triglycerides are important components of plant oils, animal fats and animal plasma lipoproteins.
    GO:0034197    triglyceride transport    The directed movement of triglyceride into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Triglycerides are important components of plant oils, animal fats and animal plasma lipoproteins.
    GO:0034372    very-low-density lipoprotein particle remodeling    The acquisition, loss or modification of a protein or lipid within a very-low-density lipoprotein particle, including the hydrolysis of triglyceride by hepatic lipase or lipoprotein lipase and the subsequent loss of free fatty acid.
cellular component
    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:0034364    high-density lipoprotein particle    A lipoprotein particle with a high density (typically 1.063-1.21 g/ml) and a diameter of 5-10 nm that contains APOAs and may contain APOCs and APOE; found in blood and carries lipids from body tissues to the liver as part of the reverse cholesterol transport process.
    GO:0031982    vesicle    Any small, fluid-filled, spherical organelle enclosed by membrane.

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