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(-) Description

Title :  STRUCTURE OF CPHPC BOUND TO SERUM AMYLOID P COMPONENT
 
Authors :  S. E. Kolstoe, M. C. Jenvey, S. P. Wood
Date :  29 May 12  (Deposition) - 19 Jun 13  (Release) - 22 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Sugar Binding Protein, Lectin, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. E. Kolstoe, M. C. Jenvey, A. Purvis, M. E. Light, D. Thompson, P. Hughes, M. B. Pepys, S. P. Wood
Interaction Of Serum Amyloid P Component With Hexanoyl Bis(D-Proline) (Cphpc)
Acta Crystallogr. , Sect. D V. 70 2232 2014
PubMed-ID: 25084341  |  Reference-DOI: 10.1107/S1399004714013455

(-) Compounds

Molecule 1 - SERUM AMYLOID P-COMPONENT
    Chains: A, B, C, D, E
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SERUM AMYLOID P COMPONENT, 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  (8, 65)

Asymmetric/Biological Unit (8, 65)
No.NameCountTypeFull Name
1ACT8Ligand/IonACETATE ION
2BMA1Ligand/IonBETA-D-MANNOSE
3CD35Ligand/IonCADMIUM ION
4GAL2Ligand/IonBETA-D-GALACTOSE
5GHE5Ligand/Ion(2R)-1-[6-[(2R)-2-CARBOXYPYRROLIDIN-1-YL]-6-OXIDANYLIDENE-HEXANOYL]PYRROLIDINE-2-CARBOXYLIC ACID
6MAN2Ligand/IonALPHA-D-MANNOSE
7NAG9Ligand/IonN-ACETYL-D-GLUCOSAMINE
8SIA3Ligand/IonO-SIALIC ACID

(-) Sites  (53, 53)

Asymmetric Unit (53, 53)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:120 , ACT A:1206 , ACT A:1208 , CD A:1212BINDING SITE FOR RESIDUE ACT A1205
02AC2SOFTWAREARG A:57 , ACT A:1205 , CD A:1212 , ACT A:1215 , HOH A:7145 , ASN D:189 , LYS E:143BINDING SITE FOR RESIDUE ACT A1206
03AC3SOFTWAREASP A:58 , ASN A:59 , LEU A:62 , TYR A:64 , TYR A:74 , GLU A:136 , ASP A:138 , GLN A:148 , CD A:1209 , CD A:1210 , HOH A:7149 , HOH A:7242 , ASP E:58 , ASN E:59 , LEU E:62 , TYR E:64 , TYR E:74 , GLU E:136 , ASP E:138 , GLN E:148 , GHE E:1207 , CD E:1208 , CD E:1209 , HOH E:7109 , HOH E:7179 , HOH E:7228 , HOH E:7229BINDING SITE FOR RESIDUE GHE A1207
04AC4SOFTWAREARG A:77 , HIS A:78 , ARG A:120 , ACT A:1205 , CD A:1212 , ACT A:1215BINDING SITE FOR RESIDUE ACT A1208
05AC5SOFTWAREGLU A:136 , ASP A:138 , GLN A:148 , GHE A:1207 , HOH A:7240 , HOH A:7242 , GHE E:1207BINDING SITE FOR RESIDUE CD A1209
06AC6SOFTWAREASP A:58 , ASN A:59 , GLU A:136 , GLN A:137 , ASP A:138 , GHE A:1207 , GHE E:1207BINDING SITE FOR RESIDUE CD A1210
07AC7SOFTWAREGLU A:14 , HOH A:7036 , HOH A:7038 , HOH A:7315 , HOH A:7316 , HOH A:7317BINDING SITE FOR RESIDUE CD A1211
08AC8SOFTWAREACT A:1205 , ACT A:1206 , ACT A:1208 , ACT A:1215BINDING SITE FOR RESIDUE CD A1212
09AC9SOFTWAREASP A:145 , SER A:147 , HOH A:7255 , HOH A:7257 , HOH A:7258 , HOH A:7262BINDING SITE FOR RESIDUE CD A1213
10BC1SOFTWAREARG A:77 , ACT A:1206 , ACT A:1208 , CD A:1212 , LYS E:143 , HOH E:7184BINDING SITE FOR RESIDUE ACT A1215
11BC2SOFTWAREHOH A:7250 , HOH A:7251 , HOH A:7253 , HOH A:7319 , HOH A:7320 , HOH A:7321BINDING SITE FOR RESIDUE CD A1216
12BC3SOFTWAREHOH A:7263 , HOH A:7316 , HOH A:7317 , HOH A:7322 , HOH A:7323 , HOH A:7324 , HOH A:7325BINDING SITE FOR RESIDUE CD A1218
13BC4SOFTWAREGLN A:55 , HOH A:7133 , HOH A:7244 , HOH A:7327 , GLU D:27BINDING SITE FOR RESIDUE CD A1219
14BC5SOFTWAREASP B:58 , ASN B:59 , LEU B:62 , TYR B:64 , TYR B:74 , GLU B:136 , ASP B:138 , GLN B:148 , CD B:1209 , CD B:1210 , HOH B:7127 , HOH B:7209 , ASP D:58 , ASN D:59 , LEU D:62 , TYR D:64 , TYR D:74 , GLU D:136 , ASP D:138 , GLN D:148 , GHE D:1207 , CD D:6040 , CD D:6041 , HOH D:7120 , HOH D:7206 , HOH D:7266BINDING SITE FOR RESIDUE GHE B1207
15BC6SOFTWAREHIS B:78 , ARG B:120 , CD B:1212 , HOH B:7122 , HOH B:7149 , HOH B:7264 , HOH B:7265BINDING SITE FOR RESIDUE ACT B1208
16BC7SOFTWAREASP B:58 , ASN B:59 , GLU B:136 , GLN B:137 , ASP B:138 , GHE B:1207 , GHE D:1207BINDING SITE FOR RESIDUE CD B1209
17BC8SOFTWAREGLU B:136 , ASP B:138 , GLN B:148 , GHE B:1207 , HOH B:7208 , HOH B:7209 , GHE D:1207BINDING SITE FOR RESIDUE CD B1210
18BC9SOFTWAREGLU B:14 , HOH B:7042 , HOH B:7043 , HOH B:7266BINDING SITE FOR RESIDUE CD B1211
19CC1SOFTWAREACT B:1208 , HOH B:7145 , HOH B:7146 , HOH B:7149 , HOH B:7264 , HOH B:7265 , HOH B:7267BINDING SITE FOR RESIDUE CD B1212
20CC2SOFTWARETHR B:2 , TYR B:190 , GLU B:191 , ILE B:192 , ARG B:193 , HOH B:7005 , HOH B:7243BINDING SITE FOR RESIDUE SIA B1213
21CC3SOFTWAREHOH B:7266 , HOH B:7269BINDING SITE FOR RESIDUE CD B1214
22CC4SOFTWAREHOH B:7216 , HOH B:7217 , HOH B:7270 , HOH B:7271 , HOH B:7272 , HOH B:7273 , HOH D:7117BINDING SITE FOR RESIDUE CD B1215
23CC5SOFTWAREHOH B:7197 , HOH B:7198 , HOH B:7274 , HOH B:7275BINDING SITE FOR RESIDUE CD B1216
24CC6SOFTWAREASP C:58 , ASN C:59 , GLU C:136 , GLN C:137 , ASP C:138 , GHE C:1207BINDING SITE FOR RESIDUE CD C1205
25CC7SOFTWAREGLU C:136 , ASP C:138 , GLN C:148 , GHE C:1207 , HOH C:7206 , HOH C:7207BINDING SITE FOR RESIDUE CD C1206
26CC8SOFTWAREASP C:58 , ASN C:59 , LEU C:62 , TYR C:64 , TYR C:74 , GLU C:136 , ASP C:138 , GLN C:148 , CD C:1205 , CD C:1206 , HOH C:7121 , HOH C:7207 , HOH C:7275BINDING SITE FOR RESIDUE GHE C1207
27CC9SOFTWAREASP C:145 , SER C:147 , HOH C:7216 , HOH C:7217 , HOH C:7218 , HOH C:7222BINDING SITE FOR RESIDUE CD C1208
28DC1SOFTWAREGLU C:14 , HOH C:7031 , HOH C:7034 , HOH C:7035 , HOH C:7276BINDING SITE FOR RESIDUE CD C1210
29DC2SOFTWAREHOH C:7034 , HOH C:7276 , HOH C:7277 , HOH C:7278 , HOH C:7279BINDING SITE FOR RESIDUE CD C1211
30DC3SOFTWAREHOH C:7141 , HOH C:7280 , HOH C:7281 , HOH C:7282 , HOH C:7283BINDING SITE FOR RESIDUE CD C1212
31DC4SOFTWAREGHE B:1207 , GLU D:136 , ASP D:138 , GLN D:148 , GHE D:1207 , HOH D:7203 , HOH D:7206BINDING SITE FOR RESIDUE CD D6040
32DC5SOFTWAREGHE B:1207 , ASP D:58 , ASN D:59 , GLU D:136 , GLN D:137 , ASP D:138 , GHE D:1207BINDING SITE FOR RESIDUE CD D6041
33DC6SOFTWAREASP D:145 , SER D:147 , HOH D:7214 , HOH D:7216 , HOH D:7219 , HOH D:7274BINDING SITE FOR RESIDUE CD D6042
34DC7SOFTWAREGLU D:14 , HOH D:7030 , HOH D:7033 , HOH D:7034 , HOH D:7275BINDING SITE FOR RESIDUE CD D6043
35DC8SOFTWARESER D:147 , HOH D:7034 , HOH D:7220 , HOH D:7221 , HOH D:7275 , HOH D:7276 , HOH D:7277BINDING SITE FOR RESIDUE CD D6044
36DC9SOFTWAREARG E:193 , CD E:1210 , ACT E:1214 , ACT E:1215 , HOH E:7215BINDING SITE FOR RESIDUE ACT E1206
37EC1SOFTWAREASP A:58 , ASN A:59 , LEU A:62 , TYR A:64 , TYR A:74 , GLU A:136 , ASP A:138 , GLN A:148 , GHE A:1207 , CD A:1209 , CD A:1210 , HOH A:7149 , HOH A:7242 , ASP E:58 , ASN E:59 , LEU E:62 , TYR E:64 , TYR E:74 , GLU E:136 , ASP E:138 , GLN E:148 , CD E:1208 , CD E:1209 , HOH E:7109 , HOH E:7179 , HOH E:7228 , HOH E:7229BINDING SITE FOR RESIDUE GHE E1207
38EC2SOFTWAREGHE A:1207 , ASP E:58 , ASN E:59 , GLU E:136 , GLN E:137 , ASP E:138 , GHE E:1207BINDING SITE FOR RESIDUE CD E1208
39EC3SOFTWAREGHE A:1207 , GLU E:136 , ASP E:138 , GLN E:148 , GHE E:1207 , HOH E:7177 , HOH E:7179BINDING SITE FOR RESIDUE CD E1209
40EC4SOFTWAREACT E:1206 , ACT E:1214 , ACT E:1215 , CD E:1218 , HOH E:7214 , HOH E:7227 , HOH E:7230BINDING SITE FOR RESIDUE CD E1210
41EC5SOFTWAREASP E:145 , SER E:147 , HOH E:7186 , HOH E:7187 , HOH E:7191 , HOH E:7231BINDING SITE FOR RESIDUE CD E1211
42EC6SOFTWAREGLU E:14 , HOH E:7032 , HOH E:7034 , HOH E:7035BINDING SITE FOR RESIDUE CD E1212
43EC7SOFTWAREACT E:1206 , CD E:1210 , ACT E:1215BINDING SITE FOR RESIDUE ACT E1214
44EC8SOFTWAREACT E:1206 , CD E:1210 , ACT E:1214 , HOH E:7050 , HOH E:7214 , HOH E:7230BINDING SITE FOR RESIDUE ACT E1215
45EC9SOFTWAREHOH E:7034 , HOH E:7192 , HOH E:7232 , HOH E:7233 , HOH E:7234BINDING SITE FOR RESIDUE CD E1216
46FC1SOFTWAREASP B:145 , SER B:147 , HOH B:7219 , HOH D:7147 , HOH E:7235 , HOH E:7236BINDING SITE FOR RESIDUE CD E1217
47FC2SOFTWARECD E:1210 , CD E:1219 , HOH E:7046 , HOH E:7227 , HOH E:7230 , HOH E:7237 , HOH E:7238BINDING SITE FOR RESIDUE CD E1218
48FC3SOFTWARECD E:1218 , HOH E:7182 , HOH E:7238 , HOH E:7239BINDING SITE FOR RESIDUE CD E1219
49FC4SOFTWAREGLN A:31 , ASN A:32 , SER A:101 , HOH A:7081 , HOH A:7082BINDING SITE FOR MONO-SACCHARIDE NAG A1214 BOUND TO ASN A 32
50FC5SOFTWAREGLN B:31 , ASN B:32 , SER B:101 , HOH B:7081BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 32 RESIDUES 1205 TO 1206
51FC6SOFTWAREGLN C:31 , ASN C:32 , GLU C:99 , SER C:101 , HOH C:7075 , HOH C:7076BINDING SITE FOR MONO-SACCHARIDE NAG C1209 BOUND TO ASN C 32
52FC8SOFTWAREASP B:58 , ASN B:59 , LEU B:62 , TYR B:64 , TYR B:74 , GLU B:136 , ASP B:138 , GLN B:148 , GHE B:1207 , CD B:1209 , CD B:1210 , HOH B:7122 , HOH B:7127 , HOH B:7209 , TYR C:190 , GLU C:191 , ILE C:192 , ARG C:193 , HOH C:7006 , HOH C:7257 , HOH C:7259 , HOH C:7261 , HOH C:7265 , GLN D:31 , ASN D:32 , ASP D:58 , ASN D:59 , LEU D:62 , TYR D:64 , TYR D:74 , SER D:101 , GLU D:136 , ASP D:138 , GLN D:148 , CD D:6040 , CD D:6041 , HOH D:7068 , HOH D:7120 , HOH D:7175 , HOH D:7206 , HOH D:7259 , HOH D:7260 , HOH D:7262 , HOH D:7263 , HOH D:7264 , HOH D:7266 , HOH D:7269 , HOH D:7270 , HOH D:7271 , HOH D:7272 , HOH D:7273 , ASN E:189 , TYR E:190 , GLU E:191 , ILE E:192 , ARG E:193BINDING SITE FOR CHAIN D OF POLYSACCHARIDE RESIDUES 1132 TO 6039
53GC1SOFTWAREGLN E:31 , ASN E:32 , HOH E:7151BINDING SITE FOR MONO-SACCHARIDE NAG E1213 BOUND TO ASN E 32

(-) 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 d4avva_ A: 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: 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)
                 4avv 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 d4avvb_ B: 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: 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)
                 4avv 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 d4avvc_ 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....hhhhhhhhhhh.......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)
                 4avv 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 d4avvd_ 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)
                 4avv 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 d4avve_ E: 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: 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)
                 4avv 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 4AVV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AVV)

(-) 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.

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  4avv
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  SAMP_HUMAN | P02743
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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 2a3x 2a3y 2w08 3d5o 3kqr 4avs 4avt 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.
2w08 THE STRUCTURE OF SERUM AMYLOID P COMPONENT BOUND TO 0-PHOSPHO-THREONINE
4avs STRUCTURE OF N-ACETYL-L-PROLINE BOUND TO SERUM AMYLOID P COMPONENT
4avt STRUCTURE OF CPHPC BOUND TO SERUM AMYLOID P COMPONENT
4ayu STRUCTURE OF N-ACETYL-D-PROLINE BOUND TO SERUM AMYLOID P COMPONENT