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

(-) Description

Title :  THE STRUCTURE OF SERUM AMYLOID P COMPONENT BOUND TO PHOSPHOETHANOLAMINE
 
Authors :  H. Mikolajek, S. E. Kolstoe, S. P. Wood, M. B. Pepys
Date :  17 Nov 09  (Deposition) - 08 Dec 10  (Release) - 23 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Glycoprotein, Amyloid, Disulfide Bond, Lectin, Metal-Binding, Secreted (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Mikolajek, S. E. Kolstoe, V. E. Pye, P. Mangione, M. B. Pepys, S. P. Wood
Structural Basis Of Ligand Specificity In The Human Pentraxins, C-Reactive Protein And Serum Amyloid P Component.
J. Mol. Recognit. V. 24 371 2011
PubMed-ID: 21360619  |  Reference-DOI: 10.1002/JMR.1090

(-) Compounds

Molecule 1 - SERUM AMYLOID P-COMPONENT
    Chains: A, B, C, D, E
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SAP, 9.5S ALPHA-1-GLYCOPROTEIN

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 20)

Asymmetric/Biological Unit (3, 20)
No.NameCountTypeFull Name
1CA10Ligand/IonCALCIUM ION
2NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
3OPE5Ligand/IonPHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU E:136 , ASP E:138 , GLN E:148 , HOH E:225 , HOH E:226 , OPE E:4700BINDING SITE FOR RESIDUE CA E 205
02AC2SOFTWAREASP E:58 , ASN E:59 , GLU E:136 , GLN E:137 , ASP E:138 , OPE E:4700BINDING SITE FOR RESIDUE CA E 206
03AC3SOFTWAREGLN A:31 , ASN A:32 , GLU A:99 , HOH A:228 , HOH A:230BINDING SITE FOR RESIDUE NAG A 207
04AC4SOFTWAREGLU D:136 , ASP D:138 , GLN D:148 , HOH D:230 , HOH D:235 , OPE D:3700BINDING SITE FOR RESIDUE CA D 205
05AC5SOFTWAREASP D:58 , ASN D:59 , GLU D:136 , GLN D:137 , ASP D:138 , OPE D:3700BINDING SITE FOR RESIDUE CA D 206
06AC6SOFTWAREGLN B:31 , ASN B:32 , GLU B:99 , VAL B:163 , HOH B:435 , HOH B:436 , HOH B:860 , HOH B:1308 , HOH B:1310BINDING SITE FOR RESIDUE NAG B 207
07AC7SOFTWAREGLU C:136 , ASP C:138 , GLN C:148 , HOH C:228 , HOH C:250 , OPE C:2700BINDING SITE FOR RESIDUE CA C 205
08AC8SOFTWAREASP C:58 , ASN C:59 , GLU C:136 , GLN C:137 , ASP C:138 , OPE C:2700BINDING SITE FOR RESIDUE CA C 206
09AC9SOFTWAREGLN C:31 , ASN C:32 , HOH C:476 , HOH C:810BINDING SITE FOR RESIDUE NAG C 207
10BC1SOFTWAREASP B:58 , ASN B:59 , GLU B:136 , GLN B:137 , ASP B:138 , OPE B:1700BINDING SITE FOR RESIDUE CA B 205
11BC2SOFTWAREGLU B:136 , ASP B:138 , GLN B:148 , HOH B:232 , HOH B:234 , OPE B:1700BINDING SITE FOR RESIDUE CA B 206
12BC3SOFTWAREGLN D:31 , ASN D:32 , GLU D:99 , HOH D:519 , HOH D:771BINDING SITE FOR RESIDUE NAG D 207
13BC4SOFTWAREGLU A:136 , ASP A:138 , GLN A:148 , HOH A:226 , HOH A:227 , OPE A:700BINDING SITE FOR RESIDUE CA A 205
14BC5SOFTWAREASP A:58 , ASN A:59 , GLU A:136 , GLN A:137 , ASP A:138 , OPE A:700BINDING SITE FOR RESIDUE CA A 206
15BC6SOFTWAREGLN E:31 , ASN E:32 , HOH E:251 , HOH E:1230BINDING SITE FOR RESIDUE NAG E 207
16BC7SOFTWAREASP A:58 , ASN A:59 , LEU A:62 , TYR A:64 , TYR A:74 , GLU A:136 , ASP A:138 , GLN A:148 , CA A:205 , CA A:206 , HOH A:227 , HOH A:605 , HOH A:752 , HOH A:847 , HOH A:923BINDING SITE FOR RESIDUE OPE A 700
17BC8SOFTWAREASP B:58 , ASN B:59 , TYR B:64 , TYR B:74 , GLU B:136 , ASP B:138 , GLN B:148 , CA B:205 , CA B:206 , HOH B:251 , HOH B:439 , HOH B:457 , HOH B:606 , HOH B:1367 , HOH B:1396BINDING SITE FOR RESIDUE OPE B 1700
18BC9SOFTWAREASP C:58 , ASN C:59 , TYR C:74 , GLU C:136 , ASP C:138 , GLN C:148 , CA C:205 , CA C:206 , HOH C:229 , HOH C:231 , HOH C:251 , HOH C:608 , HOH C:913 , HOH C:1371BINDING SITE FOR RESIDUE OPE C 2700
19CC1SOFTWAREASP D:58 , ASN D:59 , TYR D:64 , TYR D:74 , GLU D:136 , ASP D:138 , GLN D:148 , CA D:205 , CA D:206 , HOH D:252 , HOH D:257 , HOH D:610 , HOH D:906BINDING SITE FOR RESIDUE OPE D 3700
20CC2SOFTWAREASP E:58 , ASN E:59 , LEU E:62 , TYR E:64 , TYR E:74 , GLU E:136 , ASP E:138 , GLN E:148 , CA E:205 , CA E:206 , HOH E:582 , HOH E:611 , HOH E:649BINDING SITE FOR RESIDUE OPE E 4700

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:36 -A:95
2B:36 -B:95
3C:36 -C:95
4D:36 -D:95
5E:36 -E:95

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Phe A:88 -Pro A:89
2Phe B:88 -Pro B:89
3Phe C:88 -Pro C:89
4Phe D:88 -Pro D:89
5Phe E:88 -Pro E:89

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 15)

Asymmetric/Biological Unit (3, 15)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_035814G141SSAMP_HUMANUnclassified  ---A/B/C/D/EG122S
2UniProtVAR_006054E155GSAMP_HUMANPolymorphism  ---A/B/C/D/EE136G
3UniProtVAR_006055S158GSAMP_HUMANPolymorphism  ---A/B/C/D/ES139G
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 10)

Asymmetric/Biological Unit (2, 10)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PTX_2PS51828 Pentraxin (PTX) domain profile.SAMP_HUMAN24-223
 
 
 
 		  5A:5-204
B:5-204
C:5-204
D:5-204
E:5-204
2PTX_1PS00289 Pentraxin domain signature.SAMP_HUMAN112-119
 
 
 
 		  5A:93-100
B:93-100
C:93-100
D:93-100
E:93-100

(-) Exons   (2, 10)

Asymmetric/Biological Unit (2, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002550401ENSE00000904938chr1:159557615-159557775161SAMP_HUMAN1-22225A:1-3
B:1-3
C:1-3
D:1-3
E:1-3		3
3
3
3
3
1.2ENST000002550402ENSE00000904939chr1:159557891-159558655765SAMP_HUMAN22-2232025A:3-204
B:3-204
C:3-204
D:3-204
E:3-204		202
202
202
202
202

(-) 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:204
 aligned with SAMP_HUMAN | P02743 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:204
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219    
           SAMP_HUMAN    20 HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV 223
               SCOP domains d3kqra_ A: Serum amyloid P component (SAP)                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee.......eeeee........eeeeeeeee......eeeeeeee..eeeeeeeeeee..eeeeee..eeeeee........eeeeeeee....eeeeee..ee...ee...........eeee...........hhhhh..eeeeeeeee....hhhhhhhhhhh.......ee....eeeee...eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------S-------------G--G----------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----PTX_2  PDB: A:5-204 UniProt: 24-223                                                                                                                                                                      PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------PTX_1   -------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) 1.1--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --Exon 1.2  PDB: A:3-204 UniProt: 22-223                                                                                                                                                                     Transcript 1 (2)
                 3kqr A   1 HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV 204
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200    


Chain B from PDB  Type:PROTEIN  Length:204
 aligned with SAMP_HUMAN | P02743 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:204
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219    
           SAMP_HUMAN    20 HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV 223
               SCOP domains d3kqrb_ B: Serum amyloid P component (SAP)                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee.......eeeee........eeeeeeeee......eeeeeeee..eeeeeeeeeee..eeeeee..eeeeee........eeeeeeee....eeeeee..ee...ee...........eeee...........hhhhh..eeeeeeeee....hhhhhhhhhhh.......ee....eeeee...eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------S-------------G--G----------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----PTX_2  PDB: B:5-204 UniProt: 24-223                                                                                                                                                                      PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------PTX_1   -------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) 1.1--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --Exon 1.2  PDB: B:3-204 UniProt: 22-223                                                                                                                                                                     Transcript 1 (2)
                 3kqr B   1 HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV 204
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200    


Chain C from PDB  Type:PROTEIN  Length:204
 aligned with SAMP_HUMAN | P02743 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:204
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219    
           SAMP_HUMAN    20 HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV 223
               SCOP domains d3kqrc_ C: Serum amyloid P component (SAP)                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee.......eeee.........eeeeeeeee......eeeeeeee..eeeeeeeeeee..eeeeee..eeeeee........eeeeeeee....eeeeee..ee...ee...........eeee...........hhhhh..eeeeeeeee....hhhhhhhhhh........ee.....eeee...eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------S-------------G--G----------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----PTX_2  PDB: C:5-204 UniProt: 24-223                                                                                                                                                                      PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------PTX_1   -------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) 1.1--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --Exon 1.2  PDB: C:3-204 UniProt: 22-223                                                                                                                                                                     Transcript 1 (2)
                 3kqr C   1 HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV 204
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200    


Chain D from PDB  Type:PROTEIN  Length:204
 aligned with SAMP_HUMAN | P02743 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:204
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219    
           SAMP_HUMAN    20 HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV 223
               SCOP domains d3kqrd_ D: Serum amyloid P component (SAP)                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee.......eeee.........eeeeeeeee......eeeeeeee..eeeeeeeeeee..eeeeee..eeeeee........eeeeeeee....eeeeee..ee...ee...........eeee...........hhhhh..eeeeeeeee....hhhhhhhhhhh.......ee.....eeee...eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------S-------------G--G----------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----PTX_2  PDB: D:5-204 UniProt: 24-223                                                                                                                                                                      PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------PTX_1   -------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) 1.1--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --Exon 1.2  PDB: D:3-204 UniProt: 22-223                                                                                                                                                                     Transcript 1 (2)
                 3kqr D   1 HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV 204
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200    


Chain E from PDB  Type:PROTEIN  Length:204
 aligned with SAMP_HUMAN | P02743 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:204
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219    
           SAMP_HUMAN    20 HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV 223
               SCOP domains d3kqre_ E: Serum amyloid P component (SAP)                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ------Pentaxin-3kqrE01 E:7-200                                                                                                                                                                          ---- Pfam domains (1)
           Pfam domains (2) ------Pentaxin-3kqrE02 E:7-200                                                                                                                                                                          ---- Pfam domains (2)
           Pfam domains (3) ------Pentaxin-3kqrE03 E:7-200                                                                                                                                                                          ---- Pfam domains (3)
           Pfam domains (4) ------Pentaxin-3kqrE04 E:7-200                                                                                                                                                                          ---- Pfam domains (4)
           Pfam domains (5) ------Pentaxin-3kqrE05 E:7-200                                                                                                                                                                          ---- Pfam domains (5)
         Sec.struct. author ......eeeee.......eeeee........eeeeeeeee......eeeeeeee..eeeeeeeeeee..eeeeee..eeeeee........eeeeeeee....eeeeee..ee...ee...........eeee...........hhhhh..eeeeeeeee....hhhhhhhhhhh.......ee....eeeee...eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------S-------------G--G----------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----PTX_2  PDB: E:5-204 UniProt: 24-223                                                                                                                                                                      PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------PTX_1   -------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) 1.1--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --Exon 1.2  PDB: E:3-204 UniProt: 22-223                                                                                                                                                                     Transcript 1 (2)
                 3kqr E   1 HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV 204
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
   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, 5)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KQR)

(-) Pfam Domains  (1, 5)

Asymmetric/Biological Unit
(-)
Clan: Concanavalin (293)

(-) Gene Ontology  (26, 26)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E   (SAMP_HUMAN | P02743)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0001849    complement component C1q binding    Interacting selectively and non-covalently with the C1q component of the classical complement cascade.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0051082    unfolded protein binding    Interacting selectively and non-covalently with an unfolded protein.
    GO:0046790    virion binding    Interacting selectively and non-covalently with a virion, either by binding to components of the capsid or the viral envelope.
biological process
    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:0044267    cellular protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
    GO:0051131    chaperone-mediated protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex, mediated by chaperone molecules that do not form part of the finished complex.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0044869    negative regulation by host of viral exo-alpha-sialidase activity    The process in which a host organism decreases viral exo-alpha-sialidase activity, the catalysis of the hydrolysis of peptide bonds in a protein.
    GO:0044871    negative regulation by host of viral glycoprotein metabolic process    A process in which a host organism stops, prevents or reduces the frequency, rate or extent of viral glycoprotein metabolic process.
    GO:0002674    negative regulation of acute inflammatory response    Any process that stops, prevents, or reduces the frequency, rate, or extent of an acute inflammatory response.
    GO:1903016    negative regulation of exo-alpha-sialidase activity    Any process that stops, prevents or reduces the frequency, rate or extent of exo-alpha-sialidase activity.
    GO:1903019    negative regulation of glycoprotein metabolic process    Any process that stops, prevents or reduces the frequency, rate or extent of glycoprotein metabolic process.
    GO:0045656    negative regulation of monocyte differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of monocyte differentiation.
    GO:0046597    negative regulation of viral entry into host cell    Any process that stops, prevents, or reduces the frequency, rate or extent of the entry of viral entry into a host cell.
    GO:0048525    negative regulation of viral process    Any process that stops, prevents, or reduces the frequency, rate or extent of a multi-organism process in which a virus is a participant.
    GO:0061045    negative regulation of wound healing    Any process that decreases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury.
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
cellular component
    GO:0072562    blood microparticle    A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
    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:0031012    extracellular matrix    A structure lying external to one or more cells, which provides structural support for cells or tissues.
    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:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

 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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OPE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
    CC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Phe A:88 - Pro A:89   [ RasMol ]  
    Phe B:88 - Pro B:89   [ RasMol ]  
    Phe C:88 - Pro C:89   [ RasMol ]  
    Phe D:88 - Pro D:89   [ RasMol ]  
    Phe E:88 - Pro E:89   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3kqr
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SAMP_HUMAN | P02743
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  SAMP_HUMAN | P02743
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SAMP_HUMAN | P02743: 1gyk 1lgn 1sac 2a3w 2a3x 2a3y 2w08 3d5o 4avs 4avt 4avv 4ayu

(-) Related Entries Specified in the PDB File

1gyk SERUM AMYLOID P COMPONENT CO-CRYSTALLISED WITH MOBDG AT NEUTRAL PH
1lgn DECAMERIC DAMP COMPLEX OF HUMAN SERUM AMYLOID P COMPONENT
1sac SERUM AMYLOID P COMPONENT (SAP)
2a3w DECAMERIC STRUCTURE OF HUMAN SERUM AMYLOID P - COMPONENTBOUND TO BIS-1,2-{[(Z)-2- CARBOXY-2-METHYL-1,3- DIOXANE]-5- YLOXYCARBAMOYL}-ETHANE
2a3x DECAMERIC CRYSTAL STRUCTURE OF HUMAN SERUM AMYLOID P- COMPONENT BOUND TO BIS-1,2-{[(Z)-2CARBOXY- 2-METHYL-1,3- DIOXANE]- 5- YLOXYCARBONYL}-PIPERAZINE
2a3y PENTAMERIC CRYSTAL STRUCTURE OF HUMAN SERUM AMYLOID P- COMPONENT BOUND TO BIS-1,2-{[(Z)-2CARBOXY-2-METHYL-1,3- DIOXANE]-5- YLOXYCARBAMOYL}-ETHANE