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(-) Description

Title :  DECAMERIC CRYSTAL STRUCTURE OF HUMAN SERUM AMYLOID P-COMPONENT BOUND TO BIS-1,2-{[(Z)-2CARBOXY- 2-METHYL-1,3-DIOXANE]- 5-YLOXYCARBONYL}-PIPERAZINE
 
Authors :  J. G. Ho, P. I. Kitov, E. Paszkiewicz, J. Sadowska, D. R. Bundle, K. K. Ng
Date :  27 Jun 05  (Deposition) - 26 Jul 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,I,J
Keywords :  Multivalent Ligand, Serum Amyloid, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. G. Ho, P. I. Kitov, E. Paszkiewicz, J. Sadowska, D. R. Bundle, K. K. Ng
Ligand-Assisted Aggregation Of Proteins: Dimerization Of Serum Amyloid P Component By Bivalent Ligands.
J. Biol. Chem. V. 280 31999 2005
PubMed-ID: 16036920  |  Reference-DOI: 10.1074/JBC.M504403200

(-) Compounds

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

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric/Biological Unit : ABCDEFGHIJ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 23)

Asymmetric/Biological Unit (2, 23)
No.NameCountTypeFull Name
1CA20Ligand/IonCALCIUM ION
2CPK3Ligand/IonBIS-1,2-{[(Z)-2CARBOXY-2-METHYL-1,3-DIOXANE]-5-YLOXYCARBONYL}-PIPERAZINE

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:58 , ASN A:59 , GLU A:136 , GLN A:137 , ASP A:138BINDING SITE FOR RESIDUE CA A 301
02AC2SOFTWAREGLU A:136 , ASP A:138 , GLN A:148BINDING SITE FOR RESIDUE CA A 302
03AC3SOFTWAREASP B:58 , ASN B:59 , GLU B:136 , GLN B:137 , ASP B:138 , CA B:304BINDING SITE FOR RESIDUE CA B 303
04AC4SOFTWAREGLU B:136 , ASP B:138 , ASP B:145 , GLN B:148 , CA B:303BINDING SITE FOR RESIDUE CA B 304
05AC5SOFTWAREASP C:58 , ASN C:59 , GLU C:136 , GLN C:137 , ASP C:138 , CPK C:402BINDING SITE FOR RESIDUE CA C 305
06AC6SOFTWAREGLU C:136 , ASP C:138 , GLN C:148 , CPK C:402BINDING SITE FOR RESIDUE CA C 306
07AC7SOFTWAREASP D:58 , ASN D:59 , GLU D:136 , GLN D:137 , ASP D:138 , CPK I:401BINDING SITE FOR RESIDUE CA D 307
08AC8SOFTWAREGLU D:136 , ASP D:138 , GLN D:148 , CPK I:401BINDING SITE FOR RESIDUE CA D 308
09AC9SOFTWAREASP E:58 , ASN E:59 , GLU E:136 , GLN E:137 , ASP E:138 , CPK H:403BINDING SITE FOR RESIDUE CA E 309
10BC1SOFTWAREGLU E:136 , ASP E:138 , GLN E:148 , CPK H:403BINDING SITE FOR RESIDUE CA E 310
11BC2SOFTWAREASN F:59 , GLU F:136 , ASP F:138BINDING SITE FOR RESIDUE CA F 311
12BC3SOFTWAREGLU F:136 , ASP F:138 , LYS F:143 , ASP F:145 , GLN F:148BINDING SITE FOR RESIDUE CA F 312
13BC4SOFTWAREASP G:58 , ASN G:59 , GLU G:136 , GLN G:137 , ASP G:138 , CA G:314BINDING SITE FOR RESIDUE CA G 313
14BC5SOFTWAREGLU G:136 , GLN G:137 , ASP G:138 , ASP G:145 , CA G:313BINDING SITE FOR RESIDUE CA G 314
15BC6SOFTWAREASP H:58 , ASN H:59 , GLU H:136 , GLN H:137 , ASP H:138 , CPK H:403BINDING SITE FOR RESIDUE CA H 315
16BC7SOFTWAREGLU H:136 , ASP H:138 , GLN H:148 , CPK H:403BINDING SITE FOR RESIDUE CA H 316
17BC8SOFTWAREASP I:58 , ASN I:59 , GLU I:136 , GLN I:137 , ASP I:138 , CPK I:401BINDING SITE FOR RESIDUE CA I 317
18BC9SOFTWAREGLU I:136 , ASP I:138 , GLN I:148 , CPK I:401BINDING SITE FOR RESIDUE CA I 318
19CC1SOFTWARECPK C:402 , ASP J:58 , ASN J:59 , GLU J:136 , GLN J:137 , ASP J:138BINDING SITE FOR RESIDUE CA J 319
20CC2SOFTWARECPK C:402 , GLU J:136 , ASP J:138 , GLN J:148BINDING SITE FOR RESIDUE CA J 320
21CC3SOFTWAREASN D:59 , LEU D:62 , TYR D:74 , GLU D:136 , ASP D:138 , GLN D:148 , CA D:307 , CA D:308 , ASP I:58 , ASN I:59 , LEU I:62 , TYR I:74 , GLU I:136 , ASP I:138 , GLN I:148 , CA I:317 , CA I:318BINDING SITE FOR RESIDUE CPK I 401
22CC4SOFTWAREASN C:59 , LEU C:62 , TYR C:64 , TYR C:74 , LYS C:79 , GLU C:136 , ASP C:138 , GLN C:148 , CA C:305 , CA C:306 , ASN J:59 , LEU J:62 , TYR J:64 , TYR J:74 , GLU J:136 , GLN J:148 , CA J:319 , CA J:320BINDING SITE FOR RESIDUE CPK C 402
23CC5SOFTWAREASN E:59 , LEU E:62 , TYR E:64 , TYR E:74 , GLU E:136 , ASP E:138 , GLN E:148 , CA E:309 , CA E:310 , ASN H:59 , LEU H:62 , TYR H:74 , GLU H:136 , GLN H:148 , CA H:315 , CA H:316BINDING SITE FOR RESIDUE CPK H 403

(-) SS Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1A:95 -A:36
2B:95 -B:36
3C:95 -C:36
4D:95 -D:36
5E:95 -E:36
6F:95 -F:36
7G:95 -G:36
8H:95 -H:36
9I:95 -I:36
10J:95 -J:36

(-) Cis Peptide Bonds  (10, 10)

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
6Phe F:88 -Pro F:89
7Phe G:88 -Pro G:89
8Phe H:88 -Pro H:89
9Phe I:88 -Pro I:89
10Phe J:88 -Pro J:89

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 30)

Asymmetric/Biological Unit (3, 30)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_035814G141SSAMP_HUMANUnclassified  ---A/B/C/D/E/F/G/H/I/JG122S
2UniProtVAR_006054E155GSAMP_HUMANPolymorphism  ---A/B/C/D/E/F/G/H/I/JE136G
3UniProtVAR_006055S158GSAMP_HUMANPolymorphism  ---A/B/C/D/E/F/G/H/I/JS139G
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 20)

Asymmetric/Biological Unit (2, 20)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PTX_2PS51828 Pentraxin (PTX) domain profile.SAMP_HUMAN24-223
 
 
 
 
 
 
 
 
 		  10A:5-204
B:5-204
C:5-204
D:5-204
E:5-204
F:5-204
G:5-204
H:5-204
I:5-204
J:5-204
2PTX_1PS00289 Pentraxin domain signature.SAMP_HUMAN112-119
 
 
 
 
 
 
 
 
 		  10A:93-100
B:93-100
C:93-100
D:93-100
E:93-100
F:93-100
G:93-100
H:93-100
I:93-100
J:93-100

(-) Exons   (2, 20)

Asymmetric/Biological Unit (2, 20)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002550401ENSE00000904938chr1:159557615-159557775161SAMP_HUMAN1-222210A:1-3
B:1-3
C:1-3
D:1-3
E:1-3
F:1-3
G:1-3
H:1-3
I:1-3
J:1-3		3
3
3
3
3
3
3
3
3
3
1.2ENST000002550402ENSE00000904939chr1:159557891-159558655765SAMP_HUMAN22-22320210A:3-204
B:3-204
C:3-204
D:3-204
E:3-204
F:3-204
G:3-204
H:3-204
I:3-204
J:3-204		202
202
202
202
202
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 d2a3xa_ A: Serum amyloid P component (SAP)                                                                                                                                                                   SCOP domains
               CATH domains 2a3xA00 A:1-204  [code=2.60.120.200, no name defined]                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee.......eeee.........eeeeeeeee......eeeeeeee..eeeeeeeeeee..eeeeee..eeeeee........eeeeeeee....eeeeee..ee...ee...........eeee...........hhhhh..eeeeeeeee....hhhhhhhhhh...............eeee...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)
                 2a3x 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 d2a3xb_ B: Serum amyloid P component (SAP)                                                                                                                                                                   SCOP domains
               CATH domains 2a3xB00 B:1-204  [code=2.60.120.200, no name defined]                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee.......eeee..........eeeeeeee......eeeeeeee..eeeeeeeeeee..eeeeee..eeeeee........eeeeeee.....eeeeee..ee...ee...........eeee...........hhhhh..eeeeeeeee....hhhhhhhhhhh..............eeee...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)
                 2a3x 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 d2a3xc_ C: Serum amyloid P component (SAP)                                                                                                                                                                   SCOP domains
               CATH domains 2a3xC00 C:1-204  [code=2.60.120.200, no name defined]                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee.......eeee.........eeeeeeeee......eeeeeeee..eeeeeeeeeee..eeeeee..eeeeee........eeeeeeee....eeeeee..ee...ee..........eeeee...........hhhhh..eeeeeeeee....hhhhhhhhhh........ee.hhh.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)
                 2a3x 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 d2a3xd_ D: Serum amyloid P component (SAP)                                                                                                                                                                   SCOP domains
               CATH domains 2a3xD00 D:1-204  [code=2.60.120.200, no name defined]                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee.......eeeee........eeeeeeeee......eeeeeeee..eeeeeeeeeee..eeeeee..eeeeee........eeeeeeee....eeeeee.......ee...........eeee...........hhhhh..eeeeeeeee....hhhhhhhhhhh........hhhhheeeee...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)
                 2a3x 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 d2a3xe_ E: Serum amyloid P component (SAP)                                                                                                                                                                   SCOP domains
               CATH domains 2a3xE00 E:1-204  [code=2.60.120.200, no name defined]                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee.......eeee.........eeeeeeeee......eeeeeeee..eeeeeeeeeee..eeeeee..eeeeee........eeeeeeee....eeeeee..ee...ee...........eeee..................eeeeeeeee....hhhhhhhhhh........ee.....eeee...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)
                 2a3x E   1 HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV 204
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200    


Chain F 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 d2a3xf_ F: Serum amyloid P component (SAP)                                                                                                                                                                   SCOP domains
               CATH domains 2a3xF00 F:1-204  [code=2.60.120.200, no name defined]                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeee........eeee..........eeeeeeee......eeeeeeee..eeeeeeeeeee..eeeeee..eeeeee........eeeeeeee....eeeeee..ee...ee...........eeee...........hhhhh...eeeeeeee....hhhhhhhhhhh........hhhhh.eeee...eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------S-------------G--G----------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----PTX_2  PDB: F: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: F:3-204 UniProt: 22-223                                                                                                                                                                     Transcript 1 (2)
                 2a3x F   1 HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV 204
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200    


Chain G 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 d2a3xg_ G: Serum amyloid P component (SAP)                                                                                                                                                                   SCOP domains
               CATH domains 2a3xG00 G:1-204  [code=2.60.120.200, no name defined]                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee.......eeee..........eeeeeeee......eeeeeeee..eeeeeeeeeee..eeeeee..eeeeee........eeeeeee.....eeeeee..ee...ee..........eeeee...........hhhhh..eeeeeeeee....hhhhhhhhhh...............eeee...eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------S-------------G--G----------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----PTX_2  PDB: G: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: G:3-204 UniProt: 22-223                                                                                                                                                                     Transcript 1 (2)
                 2a3x G   1 HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV 204
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200    


Chain H 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 d2a3xh_ H: Serum amyloid P component (SAP)                                                                                                                                                                   SCOP domains
               CATH domains 2a3xH00 H:1-204  [code=2.60.120.200, no name defined]                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee.......eeee.........eeeeeeeee......eeeeeeee......eeeeeee..eeeeee..eeeeee........eeeeeeee....eeeeee..ee...ee..........eeeee...........hhhhh..eeeeeeeee....hhhhhhhhhh........ee.hhh.eeee...eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------S-------------G--G----------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----PTX_2  PDB: H: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: H:3-204 UniProt: 22-223                                                                                                                                                                     Transcript 1 (2)
                 2a3x H   1 HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV 204
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200    


Chain I 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 d2a3xi_ I: Serum amyloid P component (SAP)                                                                                                                                                                   SCOP domains
               CATH domains 2a3xI00 I:1-204  [code=2.60.120.200, no name defined]                                                                                                                                                        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.hhh.eeee...eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------S-------------G--G----------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----PTX_2  PDB: I: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: I:3-204 UniProt: 22-223                                                                                                                                                                     Transcript 1 (2)
                 2a3x I   1 HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV 204
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200    


Chain J 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 d2a3xj_ J: Serum amyloid P component (SAP)                                                                                                                                                                   SCOP domains
               CATH domains 2a3xJ00 J:1-204  [code=2.60.120.200, no name defined]                                                                                                                                                        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.hhh.eeee...eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------S-------------G--G----------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----PTX_2  PDB: J: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: J:3-204 UniProt: 22-223                                                                                                                                                                     Transcript 1 (2)
                 2a3x J   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, 10)

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

(-) CATH Domains  (1, 10)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Sandwich (5577)
(-)
Topology: Jelly Rolls (1293)
(-)
Homologous Superfamily: [code=2.60.120.200, no name defined] (421)
(-)
Human (Homo sapiens) (49)
1a2a3xA00A:1-204
1b2a3xB00B:1-204
1c2a3xC00C:1-204
1d2a3xD00D:1-204
1e2a3xE00E:1-204
1f2a3xF00F:1-204
1g2a3xG00G:1-204
1h2a3xH00H:1-204
1i2a3xI00I:1-204
1j2a3xJ00J:1-204

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2A3X)

(-) Gene Ontology  (26, 26)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H,I,J   (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.

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1lgn DECAMERIC DAMP COMPLEX OF HUMAN SERUM AMYLOID P COMPONENT