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(-) Description

Title :  CRYSTAL STRUCTURE OF N-TERMINAL DOMAIN OF HUMAN PLATELET RECEPTOR GLYCOPROTEIN IB-ALPHA AT 2.8 ANGSTROM RESOLUTION
 
Authors :  K. I. Varughese, Z. M. Ruggeri, R. Celikel
Date :  12 Sep 03  (Deposition) - 02 Mar 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,G
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  G  (1x)
Keywords :  Platelet Receptors, Glycocalicin, Leucine Rich Repeats, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. I. Varughese, Z. M. Ruggeri, R. Celikel
Platinum-Induced Space-Group Transformation In Crystals Of The Platelet Glycoprotein Ib Alpha N-Terminal Domain.
Acta Crystallogr. , Sect. D V. 60 405 2004
PubMed-ID: 14993663  |  Reference-DOI: 10.1107/S0907444903026805

(-) Compounds

Molecule 1 - PLATELET GLYCOPROTEIN IB ALPHA CHAIN
    ChainsA, G
    EngineeredYES
    Expression SystemDROSOPHILA MELANOGASTER
    Expression System CommonFRUIT FLY
    Expression System StrainS2
    Expression System Taxid7227
    FragmentN-TERMINAL DOMAIN
    GeneGP1BA
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGLYCOPROTEIN IBALPHA, GP-IB ALPHA, GPIBA, GPIB-ALPHA, CD42B- ALPHA, CD42B

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AG
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) G

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1MAN2Ligand/IonALPHA-D-MANNOSE
2NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
3PT3Ligand/IonPLATINUM (II) ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1MAN2Ligand/IonALPHA-D-MANNOSE
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
3PT-1Ligand/IonPLATINUM (II) ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1MAN-1Ligand/IonALPHA-D-MANNOSE
2NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
3PT-1Ligand/IonPLATINUM (II) ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:135 , LYS A:137 , ASN A:159 , NAG A:502 , GLU G:172 , HIS G:195BINDING SITE FOR RESIDUE NAG A 501
2AC2SOFTWARENAG A:501 , MAN A:503 , GLU G:172 , HIS G:195BINDING SITE FOR RESIDUE NAG A 502
3AC3SOFTWARENAG A:502 , MAN A:504 , LEU G:171 , GLU G:172 , LEU G:174 , HIS G:195BINDING SITE FOR RESIDUE MAN A 503
4AC4SOFTWAREMAN A:503 , LEU G:168 , PHE G:192 , GLY G:193 , HIS G:195 , LEU G:196 , LEU G:197BINDING SITE FOR RESIDUE MAN A 504
5AC5SOFTWAREGLU G:135 , LYS G:137 , ASN G:159 , HOH G:606 , HOH G:615BINDING SITE FOR RESIDUE NAG G 601
6AC6SOFTWAREHIS G:86 , PHE G:109BINDING SITE FOR RESIDUE PT G 602
7AC7SOFTWAREHIS A:86 , PHE A:109BINDING SITE FOR RESIDUE PT A 505
8AC8SOFTWAREGLU A:172 , HIS A:195 , HOH A:507BINDING SITE FOR RESIDUE PT A 506

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:4 -A:17
2A:209 -A:248
3A:211 -A:264
4G:4 -G:17
5G:209 -G:248
6G:211 -G:264

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (12, 24)

Asymmetric Unit (12, 24)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_011909R72HGP1BA_HUMANPolymorphism6068A/GR56H
02UniProtVAR_014206L73FGP1BA_HUMANDisease (BSS)121908063A/GL57F
03UniProtVAR_005256C81RGP1BA_HUMANDisease (BSS)781541857A/GA65R
04UniProtVAR_013511L86FGP1BA_HUMANPolymorphism13306411A/GL70F
05UniProtVAR_014207L145PGP1BA_HUMANDisease (BSS)771048666A/GL129P
06UniProtVAR_005257T161MGP1BA_HUMANPolymorphism6065A/GT145M
07UniProtVAR_005258A172VGP1BA_HUMANDisease (BSS)121908065A/GA156V
08UniProtVAR_005260C225SGP1BA_HUMANDisease (BSS)  ---A/GC209S
09UniProtVAR_019657G249SGP1BA_HUMANDisease (VWDP)  ---A/GG233S
10UniProtVAR_005261G249VGP1BA_HUMANDisease (VWDP)121908062A/GG233V
11UniProtVAR_011910A254SGP1BA_HUMANPolymorphism382524A/GA238S
12UniProtVAR_005262M255VGP1BA_HUMANDisease (VWDP)121908064A/GM239V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (12, 12)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_011909R72HGP1BA_HUMANPolymorphism6068AR56H
02UniProtVAR_014206L73FGP1BA_HUMANDisease (BSS)121908063AL57F
03UniProtVAR_005256C81RGP1BA_HUMANDisease (BSS)781541857AA65R
04UniProtVAR_013511L86FGP1BA_HUMANPolymorphism13306411AL70F
05UniProtVAR_014207L145PGP1BA_HUMANDisease (BSS)771048666AL129P
06UniProtVAR_005257T161MGP1BA_HUMANPolymorphism6065AT145M
07UniProtVAR_005258A172VGP1BA_HUMANDisease (BSS)121908065AA156V
08UniProtVAR_005260C225SGP1BA_HUMANDisease (BSS)  ---AC209S
09UniProtVAR_019657G249SGP1BA_HUMANDisease (VWDP)  ---AG233S
10UniProtVAR_005261G249VGP1BA_HUMANDisease (VWDP)121908062AG233V
11UniProtVAR_011910A254SGP1BA_HUMANPolymorphism382524AA238S
12UniProtVAR_005262M255VGP1BA_HUMANDisease (VWDP)121908064AM239V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (12, 12)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_011909R72HGP1BA_HUMANPolymorphism6068GR56H
02UniProtVAR_014206L73FGP1BA_HUMANDisease (BSS)121908063GL57F
03UniProtVAR_005256C81RGP1BA_HUMANDisease (BSS)781541857GA65R
04UniProtVAR_013511L86FGP1BA_HUMANPolymorphism13306411GL70F
05UniProtVAR_014207L145PGP1BA_HUMANDisease (BSS)771048666GL129P
06UniProtVAR_005257T161MGP1BA_HUMANPolymorphism6065GT145M
07UniProtVAR_005258A172VGP1BA_HUMANDisease (BSS)121908065GA156V
08UniProtVAR_005260C225SGP1BA_HUMANDisease (BSS)  ---GC209S
09UniProtVAR_019657G249SGP1BA_HUMANDisease (VWDP)  ---GG233S
10UniProtVAR_005261G249VGP1BA_HUMANDisease (VWDP)121908062GG233V
11UniProtVAR_011910A254SGP1BA_HUMANPolymorphism382524GA238S
12UniProtVAR_005262M255VGP1BA_HUMANDisease (VWDP)121908064GM239V

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

(-) PROSITE Motifs  (1, 12)

Asymmetric Unit (1, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LRRPS51450 Leucine-rich repeat profile.GP1BA_HUMAN72-93
 
94-115
 
117-137
 
141-162
 
165-186
 
189-210
 
  12A:56-77
G:56-77
A:78-99
G:78-99
A:101-121
G:101-121
A:125-146
G:125-146
A:149-170
G:149-170
A:173-194
G:173-194
Biological Unit 1 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LRRPS51450 Leucine-rich repeat profile.GP1BA_HUMAN72-93
 
94-115
 
117-137
 
141-162
 
165-186
 
189-210
 
  6A:56-77
-
A:78-99
-
A:101-121
-
A:125-146
-
A:149-170
-
A:173-194
-
Biological Unit 2 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LRRPS51450 Leucine-rich repeat profile.GP1BA_HUMAN72-93
 
94-115
 
117-137
 
141-162
 
165-186
 
189-210
 
  6-
G:56-77
-
G:78-99
-
G:101-121
-
G:125-146
-
G:149-170
-
G:173-194

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2bENST000003291252bENSE00001299958chr17:4835900-48371501251GP1BA_HUMAN1-4174172A:1-266
G:1-266
266
266
1.3aENST000003291253aENSE00001488421chr17:4837187-4837858672GP1BA_HUMAN418-6402230--

(-) Sequences/Alignments

Asymmetric 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:266
 aligned with GP1BA_HUMAN | P07359 from UniProtKB/Swiss-Prot  Length:652

    Alignment length:266
                                    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      
          GP1BA_HUMAN    17 HPICEVSKVASHLEVNCDKRNLTALPPDLPKDTTILHLSENLLYTFSLATLMPYTRLTQLNLDRCELTKLQVDGTLPVLGTLDLSHNQLQSLPLLGQTLPALTVLDVSFNRLTSLPLGALRGLGELQELYLKGNELKTLPPGLLTPTPKLEKLSLANNNLTELPAGLLNGLENLDTLLLQENSLYTIPKGFFGSHLLPFAFLHGNPWLCNCEILYFRRWLQDNAENVYVWKQGVDVKAMTSNVASVQCDNSDKFPVYKYPGKGCPT 282
               SCOP domains d1qyya_ A: von Willebrand factor binding domain of glycoprotein Ib alpha                                                                                                                                                                                                   SCOP domains
               CATH domains 1qyyA00 A:1-266 Ribonuclease Inhibitor                                                                                                                                                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee......eeee................eeeee.......eee.hhhh......eee.......eee.........eee....................eee.....................eee.....................eee.....................eee....................eee........hhhhhhhhhhhhhhhhhh..............hhhhhhhhhh...hhhhh....... Sec.struct. author
             SAPs(SNPs) (1) -------------------------------------------------------HF-------R----F----------------------------------------------------------P---------------M----------V----------------------------------------------------S-----------------------S----SV--------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V--------------------------------- SAPs(SNPs) (2)
                    PROSITE -------------------------------------------------------LRR  PDB: A:56-77     LRR  PDB: A:78-99     -LRR  PDB: A:101-121  ---LRR  PDB: A:125-146   --LRR  PDB: A:149-170   --LRR  PDB: A:173-194   ------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.2b  PDB: A:1-266 UniProt: 1-417 [INCOMPLETE]                                                                                                                                                                                                                        Transcript 1
                 1qyy A   1 HPICEVSKVASHLEVNCDKRNLTALPPDLPKDTTILHLSENLLYTFSLATLMPYTRLTQLNLDRAELTKLQVDGTLPVLGTLDLSHNQLQSLPLLGQTLPALTVLDVSFNRLTSLPLGALRGLGELQELYLKGNELKTLPPGLLTPTPKLEKLSLANNNLTELPAGLLNGLENLDTLLLQENSLYTIPKGFFGSHLLPFAFLHGNPWLCNCEILYFRRWLQDNAENVYVWKQGVDVKAMTSNVASVQCDNSDKFPVYKYPGKGCPT 266
                                    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      

Chain G from PDB  Type:PROTEIN  Length:266
 aligned with GP1BA_HUMAN | P07359 from UniProtKB/Swiss-Prot  Length:652

    Alignment length:266
                                    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      
          GP1BA_HUMAN    17 HPICEVSKVASHLEVNCDKRNLTALPPDLPKDTTILHLSENLLYTFSLATLMPYTRLTQLNLDRCELTKLQVDGTLPVLGTLDLSHNQLQSLPLLGQTLPALTVLDVSFNRLTSLPLGALRGLGELQELYLKGNELKTLPPGLLTPTPKLEKLSLANNNLTELPAGLLNGLENLDTLLLQENSLYTIPKGFFGSHLLPFAFLHGNPWLCNCEILYFRRWLQDNAENVYVWKQGVDVKAMTSNVASVQCDNSDKFPVYKYPGKGCPT 282
               SCOP domains d1qyyg_ G: von Willebrand factor binding domain of glycoprotein Ib alpha                                                                                                                                                                                                   SCOP domains
               CATH domains 1qyyG00 G:1-266 Ribonuclease Inhibitor                                                                                                                                                                                                                                     CATH domains
           Pfam domains (1) --LRRNT-1qyyG09 G:3-30        ------------------------LRR_7-1qyyG03 G:55-77  LRR_1-1qyyG01       --------------------------------------------------LRR_8-1qyyG05 G:148-197                           --------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --LRRNT-1qyyG10 G:3-30        ------------------------LRR_7-1qyyG04 G:55-77  LRR_1-1qyyG02       --------------------------------------------------LRR_8-1qyyG06 G:148-197                           --------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------------------------------------------------------------------------------------LRR_8-1qyyG07 G:148-197                           --------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------------------------------------------------------------------------------------------------LRR_8-1qyyG08 G:148-197                           --------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author .............eee..................eee.......eee.hhhh......eee.......eee.........eee....................eee.....................eee.....................eee.....................eee....................eee........hhhhhhhhhhhhhhhhhh..............hhhhhhhhhh...hhhhh....... Sec.struct. author
             SAPs(SNPs) (1) -------------------------------------------------------HF-------R----F----------------------------------------------------------P---------------M----------V----------------------------------------------------S-----------------------S----SV--------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V--------------------------------- SAPs(SNPs) (2)
                    PROSITE -------------------------------------------------------LRR  PDB: G:56-77     LRR  PDB: G:78-99     -LRR  PDB: G:101-121  ---LRR  PDB: G:125-146   --LRR  PDB: G:149-170   --LRR  PDB: G:173-194   ------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.2b  PDB: G:1-266 UniProt: 1-417 [INCOMPLETE]                                                                                                                                                                                                                        Transcript 1
                 1qyy G   1 HPICEVSKVASHLEVNCDKRNLTALPPDLPKDTTILHLSENLLYTFSLATLMPYTRLTQLNLDRAELTKLQVDGTLPVLGTLDLSHNQLQSLPLLGQTLPALTVLDVSFNRLTSLPLGALRGLGELQELYLKGNELKTLPPGLLTPTPKLEKLSLANNNLTELPAGLLNGLENLDTLLLQENSLYTIPKGFFGSHLLPFAFLHGNPWLCNCEILYFRRWLQDNAENVYVWKQGVDVKAMTSNVASVQCDNSDKFPVYKYPGKGCPT 266
                                    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      

   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 Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (4, 10)

Asymmetric Unit
(-)
Clan: LRR (77)

(-) Gene Ontology  (24, 24)

Asymmetric Unit(hide GO term definitions)
Chain A,G   (GP1BA_HUMAN | P07359)
molecular function
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004860    protein kinase inhibitor activity    Stops, prevents or reduces the activity of a protein kinase, an enzyme which phosphorylates a protein.
    GO:0015057    thrombin-activated receptor activity    A G-protein-coupled receptor activity that is activated by cleavage by thrombin, which exposes a tethered ligand corresponding to the new N-terminus, which binds to the receptor and activates it.
biological process
    GO:0007596    blood coagulation    The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
    GO:0007597    blood coagulation, intrinsic pathway    A protein activation cascade that contributes to blood coagulation and consists of the interactions among high molecular weight kininogen, prekallikrein, and factor XII that lead to the activation of clotting factor X.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0000902    cell morphogenesis    The developmental process in which the size or shape of a cell is generated and organized.
    GO:0007166    cell surface receptor signaling pathway    A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0019221    cytokine-mediated signaling pathway    A series of molecular signals initiated by the binding of a cytokine to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0042730    fibrinolysis    A process that solubilizes fibrin in the bloodstream of a multicellular organism, chiefly by the proteolytic action of plasmin.
    GO:0007599    hemostasis    The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
    GO:0046426    negative regulation of JAK-STAT cascade    Any process that stops, prevents, or reduces the frequency, rate or extent of the JAK-STAT signaling pathway activity.
    GO:0006469    negative regulation of protein kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity.
    GO:0030168    platelet activation    A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug.
    GO:0030193    regulation of blood coagulation    Any process that modulates the frequency, rate or extent of blood coagulation.
    GO:0070493    thrombin-activated receptor signaling pathway    The series of molecular signals generated as a consequence of a thrombin-activated receptor binding to one of its physiological ligands.
cellular component
    GO:0031362    anchored component of external side of plasma membrane    The component of the plasma membrane consisting of the gene products that are tethered to the external side of the membrane only by a covalently attached anchor, such as a lipid group embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    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:0016021    integral component of membrane    The component of a 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: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.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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  GP1BA_HUMAN | P07359
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 Related Entries

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

UniProtKB/Swiss-Prot
        GP1BA_HUMAN | P073591gwb 1k13 1m0z 1m10 1ook 1p8v 1p9a 1sq0 1u0n 2bp3 3p72 3pmh 4c2a 4c2b 4ch2 4ch8 4mgx 4yr6

(-) Related Entries Specified in the PDB File

1ook CRYSTAL STRUCTURE OF THE COMPLEX N-TERMINAL DOMAIN OF HUMAN PLATELET RECEPTOR GLYCOPROTEIN IB-ALPHA AND HUMAN ALPHA- THROMBIN RESOLUTION
1p9a CRYSTAL STRUCTURE OF N-TERMINAL DOMAIN OF HUMAN PLATELET RECEPTOR GLYCOPROTEIN IB-ALPHA AT 1.7 ANGSTROM RESOLUTION, TETRAGONAL P4(3) FORM.