Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  HUMAN FACTOR VIII C2 DOMAIN COMPLEXED TO HUMAN MONOCLONAL BO2C11 FAB.
 
Authors :  P. C. Spiegel Jr. , M. Jacquemin, J. M. Saint-Remy, B. L. Stoddard, K. P. Pratt
Date :  21 Jul 01  (Deposition) - 15 Aug 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Factor Viii, C2 Domain, Antibody, Blood Coagulation, Inhibitor, Bo2C11, Immune System/Blood Clotting Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. C. Spiegel Jr. , M. Jacquemin, J. M. Saint-Remy, B. L. Stoddard, K. P. Pratt
Structure Of A Factor Viii C2 Domain-Immunoglobulin G4Kappa Fab Complex: Identification Of An Inhibitory Antibody Epitope On The Surface Of Factor Viii.
Blood V. 98 13 2001
PubMed-ID: 11418455  |  Reference-DOI: 10.1182/BLOOD.V98.1.13
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HUMAN MONOCLONAL BO2C11 FAB LIGHT CHAIN
    ChainsA
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    StrainBO2C11
 
Molecule 2 - HUMAN MONOCLONAL BO2C11 FAB HEAVY CHAIN
    ChainsB
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    StrainBO2C11
 
Molecule 3 - HUMAN FACTOR VIII
    ChainsC
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System PlasmidPPIC9K
    Expression System StrainGS115
    Expression System Taxid4922
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL DOMAIN
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCOAGULATION FACTOR VII

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1IQD)

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:23 -A:89
2A:135 -A:195
3B:22 -B:93
4B:141 -B:197
5C:2174 -C:2326

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Ser A:7 -Pro A:8
2Tyr A:141 -Pro A:142
3Asp B:97 -Pro B:98
4Phe B:147 -Pro B:148
5Glu B:149 -Pro B:150
6Asp C:2298 -Pro C:2299

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (48, 48)

Asymmetric/Biological Unit (48, 48)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_017341C2193GFA8_HUMANDisease (HEMA)  ---CC2174G
02UniProtVAR_028690P2196RFA8_HUMANDisease (HEMA)  ---CP2177R
03UniProtVAR_028691G2198VFA8_HUMANDisease (HEMA)  ---CG2179V
04UniProtVAR_028692E2200DFA8_HUMANDisease (HEMA)  ---CE2181D
05UniProtVAR_001197I2204TFA8_HUMANDisease (HEMA)  ---CI2185T
06UniProtVAR_001198I2209NFA8_HUMANDisease (HEMA)  ---CI2190N
07UniProtVAR_001199A2211PFA8_HUMANDisease (HEMA)137852468CA2192P
08UniProtVAR_028693A2220PFA8_HUMANDisease (HEMA)782548763CA2201P
09UniProtVAR_028695P2224LFA8_HUMANDisease (HEMA)  ---CP2205L
10UniProtVAR_001201R2228GFA8_HUMANDisease (HEMA)137852355CR2209G
11UniProtVAR_001202R2228LFA8_HUMANDisease (HEMA)137852358CR2209L
12UniProtVAR_028696R2228PFA8_HUMANDisease (HEMA)  ---CR2209P
13UniProtVAR_001203R2228QFA8_HUMANDisease (HEMA)137852358CR2209Q
14UniProtVAR_028697L2229FFA8_HUMANDisease (HEMA)  ---CL2210F
15UniProtVAR_001204V2242MFA8_HUMANPolymorphism782654096CV2223M
16UniProtVAR_001205W2248CFA8_HUMANDisease (HEMA)137852469CW2229C
17UniProtVAR_028698W2248SFA8_HUMANDisease (HEMA)  ---CW2229S
18UniProtVAR_028699V2251AFA8_HUMANDisease (HEMA)782479558CV2232A
19UniProtVAR_028700V2251EFA8_HUMANDisease (HEMA)  ---CV2232E
20UniProtVAR_021356M2257VFA8_HUMANPolymorphism1800297CM2238V
21UniProtVAR_028701T2264AFA8_HUMANDisease (HEMA)  ---CT2245A
22UniProtVAR_001206Q2265RFA8_HUMANDisease (HEMA)137852470CQ2246R
23UniProtVAR_028702F2279CFA8_HUMANDisease (HEMA)  ---CF2260C
24UniProtVAR_028703F2279IFA8_HUMANDisease (HEMA)782717799CF2260I
25UniProtVAR_028704I2281TFA8_HUMANDisease (HEMA)  ---CI2262T
26UniProtVAR_065323D2286GFA8_HUMANDisease (HEMA)  ---CD2267G
27UniProtVAR_028705W2290LFA8_HUMANDisease (HEMA)  ---CW2271L
28UniProtVAR_028706G2304VFA8_HUMANDisease (HEMA)  ---CG2285V
29UniProtVAR_015134D2307AFA8_HUMANDisease (HEMA)  ---CD2288A
30UniProtVAR_001207P2319LFA8_HUMANDisease (HEMA)137852472CP2300L
31UniProtVAR_001208P2319SFA8_HUMANDisease (HEMA)137852374CP2300S
32UniProtVAR_001209R2323CFA8_HUMANDisease (HEMA)137852473CR2304C
33UniProtVAR_028707R2323GFA8_HUMANDisease (HEMA)  ---CR2304G
34UniProtVAR_001210R2323HFA8_HUMANDisease (HEMA)137852474CR2304H
35UniProtVAR_028708R2323LFA8_HUMANDisease (HEMA)  ---CR2304L
36UniProtVAR_028709R2326GFA8_HUMANDisease (HEMA)  ---CR2307G
37UniProtVAR_001211R2326LFA8_HUMANDisease (HEMA)137852360CR2307L
38UniProtVAR_028710R2326PFA8_HUMANDisease (HEMA)  ---CR2307P
39UniProtVAR_001212R2326QFA8_HUMANDisease (HEMA)137852360CR2307Q
40UniProtVAR_028711Q2330PFA8_HUMANDisease (HEMA)  ---CQ2311P
41UniProtVAR_028712W2332RFA8_HUMANDisease (HEMA)  ---CW2313R
42UniProtVAR_065324I2336FFA8_HUMANDisease (HEMA)  ---CI2317F
43UniProtVAR_028713R2339TFA8_HUMANDisease (HEMA)  ---CR2320T
44UniProtVAR_008968G2344CFA8_HUMANDisease (HEMA)  ---CG2325C
45UniProtVAR_065325G2344DFA8_HUMANDisease (HEMA)  ---CG2325D
46UniProtVAR_028714G2344SFA8_HUMANDisease (HEMA)  ---CG2325S
47UniProtVAR_028715C2345SFA8_HUMANDisease (HEMA)  ---CC2326S
48UniProtVAR_028716C2345YFA8_HUMANDisease (HEMA)  ---CC2326Y

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FA58C_3PS50022 Coagulation factors 5/8 type C domain (FA58C) profile.FA8_HUMAN2040-2188
2193-2345
  1-
C:2174-2326
2FA58C_1PS01285 Coagulation factors 5/8 type C domain (FA58C) signature 1.FA8_HUMAN2080-2107
2237-2266
  1-
C:2218-2247
3FA58C_2PS01286 Coagulation factors 5/8 type C domain (FA58C) signature 2.FA8_HUMAN2172-2188
2329-2345
  1-
C:2310-2326

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000003602562aENSE00001645223X:154251028-154250685344FA8_HUMAN1-48480--
1.3ENST000003602563ENSE00001422135X:154227875-154227754122FA8_HUMAN48-89420--
1.4ENST000003602564ENSE00001096342X:154225370-154225248123FA8_HUMAN89-130420--
1.5bENST000003602565bENSE00002195289X:154221423-154221211213FA8_HUMAN130-201720--
1.6ENST000003602566ENSE00001633063X:154215580-15421551269FA8_HUMAN201-224240--
1.7bENST000003602567bENSE00002147243X:154213078-154212962117FA8_HUMAN224-263400--
1.8ENST000003602568ENSE00001653886X:154197827-154197606222FA8_HUMAN263-337750--
1.9aENST000003602569aENSE00001776938X:154194962-154194701262FA8_HUMAN337-424880--
1.10aENST0000036025610aENSE00001708410X:154194416-154194245172FA8_HUMAN424-481580--
1.11ENST0000036025611ENSE00001607410X:154189443-15418935094FA8_HUMAN482-513320--
1.12ENST0000036025612ENSE00001748476X:154185446-154185232215FA8_HUMAN513-584720--
1.13ENST0000036025613ENSE00001769821X:154182317-154182167151FA8_HUMAN585-635510--
1.14ENST0000036025614ENSE00001591329X:154176182-154175973210FA8_HUMAN635-705710--
1.15bENST0000036025615bENSE00001311652X:154159951-1541568463106FA8_HUMAN705-174010360--
1.16ENST0000036025616ENSE00001096353X:154134848-154134695154FA8_HUMAN1740-1791520--
1.17ENST0000036025617ENSE00001096366X:154133298-154133086213FA8_HUMAN1792-1862710--
1.18ENST0000036025618ENSE00001096327X:154132799-154132571229FA8_HUMAN1863-1939770--
1.19ENST0000036025619ENSE00001096346X:154132363-154132181183FA8_HUMAN1939-2000620--
1.20ENST0000036025620ENSE00001297698X:154130442-154130326117FA8_HUMAN2000-2039400--
1.21ENST0000036025621ENSE00001413135X:154129717-15412964672FA8_HUMAN2039-2063250--
1.22ENST0000036025622ENSE00001411839X:154128226-15412814186FA8_HUMAN2063-2091290--
1.23ENST0000036025623ENSE00001403942X:154124507-154124352156FA8_HUMAN2092-2143520--
1.25ENST0000036025625ENSE00001308463X:154091502-154091358145FA8_HUMAN2144-2192490--
1.26ENST0000036025626ENSE00001096349X:154090141-154089993149FA8_HUMAN2192-2241501C:2174-222249
1.27ENST0000036025627ENSE00001096386X:154088883-154088707177FA8_HUMAN2242-2300591C:2223-228159
1.28aENST0000036025628aENSE00001878069X:154066027-1540640701958FA8_HUMAN2301-2351511C:2282-232948

(-) 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:208
                                                                                                                                                                                                                                                 
               SCOP domains d1iqda1 A:2-108 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d1iqda2 A:109-212 Immunoglobulin light chain kappa constant domain, CL-kappa                          SCOP domains
               CATH domains 1iqdA01 A:2-109 Immunoglobulins                                                                             1iqdA02 A:110-211 Immunoglobulins                                                                  - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee.....eeeeeeeeeeehhh.eeeeee......eeeee...ee.......eeeeeeeeeeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.....eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1iqd A    2 IALTQSPGTLSLSPGERATLSCRASQSFSSSYLAWYQQKPGQAPRLLIYGASTRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQKYGTSAITFGQGTRLEIKGTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLVTKSFNR  212
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201||      
                                                                                                                                                                                                                                  202|      
                                                                                                                                                                                                                                   206      

Chain B from PDB  Type:PROTEIN  Length:200
                                                                                                                                                                                                                                         
               SCOP domains d1iqdb1 B:1-114 Immunoglobulin heavy chain variable domain, VH                                                       d1iqdb2 B:115-212 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma     SCOP domains
               CATH domains 1iqdB01 B:1-114 Immunoglobulins                                                                                      1iqdB02 B:115-210 Immunoglobulins                                                -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeee.......ee...eeeee........eeeee...eeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeee....eeeeeeehhhheeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1iqd B    1 QVQLVQSGAEVKKPGASVKVSCKVSGYTLTELPVHWVRQAPGKGLEWVGSFDPESGESIYAREFQGSVTMTADTSTNIAYMELSSLRSDDTAVYYCAVPDPDAFDIWGQGTMVTVSSASTKGPSVFPLATAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVTATYTCNVDHKPSNTKVDKRV  212
                                    10        20        30        40        50        60        70        80   |||  87        97       107       117       136       146       156       166       176       192       202       212
                                                                                                             83A||                                        126|                                              185|                    
                                                                                                              83B|                                         136                                               192                    
                                                                                                               83C                                                                                                                  

Chain C from PDB  Type:PROTEIN  Length:156
 aligned with FA8_HUMAN | P00451 from UniProtKB/Swiss-Prot  Length:2351

    Alignment length:156
                                  2202      2212      2222      2232      2242      2252      2262      2272      2282      2292      2302      2312      2322      2332      2342      
           FA8_HUMAN   2193 CSMPLGMESKAISDAQITASSYFTNMFATWSPSKARLHLQGRSNAWRPQVNNPKEWLQVDFQKTMKVTGVTTQGVKSLLTSMYVKEFLISSSQDGHQWTLFFQNGKVKVFQGNQDSFTPVVNSLDPPLLTRYLRIHPQSWVHQIALRMEVLGCEAQ 2348
               SCOP domains d1iqdc_ C: C2 domain of factor VIII                                                                                                                          SCOP domains
               CATH domains 1iqdC00 C:2174-2329 Galactose-binding domain-like                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee........hhh.eee....ee..ee.hhhhh.....................eeeeeeeeeeeeeeeee.ee....eeeeeeeeeeee......ee.ee..ee..ee........eeeeeeeeeeeeeeeeeeeeee.....eeeeeeee.. Sec.struct. author
             SAPs(SNPs) (1) G--R-V-D---T----N-P--------P---L---GF------------M-----C--A-----V------AR-------------C-T----G---L-------------V--A-----------L---C--G---P-R---F--T----CS--- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------------L-------------------S--E---------------------------I---------------------------------------S---G--L-----------------DY--- SAPs(SNPs) (2)
             SAPs(SNPs) (3) -----------------------------------P----------------------------------------------------------------------------------------------H--P-----------------S---- SAPs(SNPs) (3)
             SAPs(SNPs) (4) -----------------------------------Q----------------------------------------------------------------------------------------------L--Q---------------------- SAPs(SNPs) (4)
                PROSITE (1) FA58C_3  PDB: C:2174-2326 UniProt: 2193-2345                                                                                                             --- PROSITE (1)
                PROSITE (2) --------------------------------------------FA58C_1  PDB: C:2218-2247     --------------------------------------------------------------FA58C_2          --- PROSITE (2)
               Transcript 1 Exon 1.26  PDB: C:2174-2222 UniProt: 2192-2241   Exon 1.27  PDB: C:2223-2281 UniProt: 2242-2300             Exon 1.28a  PDB: C:2282-2329 UniProt: 2301-2351  Transcript 1
                1iqd C 2174 CSMPLGMESKAISDAQITASSYFTNMFATWSPSKARLHLQGRSNAWRPQVNNPKEWLQVDFQKTMKVTGVTTQGVKSLLTSMYVKEFLISSSQDGHQWTLFFQNGKVKVFQGNQDSFTPVVNCLDPPLLTRYLRIHPQSWVHQIALRMEVLGCEAQ 2329
                                  2183      2193      2203      2213      2223      2233      2243      2253      2263      2273      2283      2293      2303      2313      2323      

   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  (5, 5)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 5)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain C   (FA8_HUMAN | P00451)
molecular function
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    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).
biological process
    GO:0048208    COPII vesicle coating    The addition of COPII proteins and adaptor proteins to ER membranes during the formation of transport vesicles, forming a vesicle coat.
    GO:0006888    ER to Golgi vesicle-mediated transport    The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
    GO:0006953    acute-phase response    An acute inflammatory response that involves non-antibody proteins whose concentrations in the plasma increase in response to infection or injury of homeothermic animals.
    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:0007599    hemostasis    The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    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:0002576    platelet degranulation    The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
cellular component
    GO:0030134    COPII-coated ER to Golgi transport vesicle    A vesicle with a coat formed of the COPII coat complex proteins. The COPII coat complex is formed by the Sec23p/Sec24p and the Sec13p/Sec31p heterodimers. COPII-associated vesicles transport proteins from the rough endoplasmic reticulum to the Golgi apparatus (anterograde transport).
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0005788    endoplasmic reticulum lumen    The volume enclosed by the membranes of the endoplasmic reticulum.
    GO:0033116    endoplasmic reticulum-Golgi intermediate compartment membrane    The lipid bilayer surrounding any of the compartments of the endoplasmic reticulum (ER)-Golgi intermediate compartment system.
    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: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.
    GO:0031093    platelet alpha granule lumen    The volume enclosed by the membrane of the platelet alpha granule.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1iqd)
 
  Sites
(no "Sites" information available for 1iqd)
 
  Cis Peptide Bonds
    Asp B:97 - Pro B:98   [ RasMol ]  
    Asp C:2298 - Pro C:2299   [ RasMol ]  
    Glu B:149 - Pro B:150   [ RasMol ]  
    Phe B:147 - Pro B:148   [ RasMol ]  
    Ser A:7 - Pro A:8   [ RasMol ]  
    Tyr A:141 - Pro A:142   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1iqd
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  FA8_HUMAN | P00451
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  306700
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  FA8_HUMAN | P00451
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        FA8_HUMAN | P004511cfg 1d7p 1fac 2r7e 3cdz 3hnb 3hny 3hob 3j2q 3j2s 4bdv 4ki5 4pt6 4xzu 5k8d

(-) Related Entries Specified in the PDB File

1d7p 1D7P CONTAINS CRYSTAL STRUCTURE OF FREE FACTOR VIII C2 DOMAIN.