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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   THE STRUCTURE OF SERUM AMYLOID P COMPONENT BOUND TO 0-PHOSPHO-THREONINE

Authors :   S. E. Kolstoe, M. B. Pepys, S. P. Wood

Date :   12 Aug 08 (Deposition) - 14 Apr 09 (Release) - 19 May 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym./Biol. Unit : A,B,C,D,E

Keywords :   Glycoprotein, Polymorphism, Metal-Binding, Tau, Lectin, Calcium, Amyloid, Secreted, Alzheimers (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. E. Kolstoe, B. H. Ridha, V. Bellotti, N. Wang, C. V. Robinson, S. J. Crutch, G. Keir, R. Kukkastenvehmas, J. R. Gallimore, W. L. Hutchinson, P. N. Hawkins, S. P. Wood, M. N. Rossor, M. B. Pepys
Molecular Dissection Of Alzheimer'S Disease Neuropathology By Depletion Of Serum Amyloid P Component.
Proc. Natl. Acad. Sci. Usa V. 106 7619 2009
PubMed-ID: 19372378 | Reference-DOI: 10.1073/PNAS.0902640106

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

		1	2	3	4	5
Asymmetric/Biological Unit	:	A	B	C	D	E

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 20)

No.	Name	Count	Type	Full Name
1	CA	10	Ligand/Ion	CALCIUM ION
2	NAG	5	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	TPO	5	Mod. Residue	PHOSPHOTHREONINE

Asymmetric Unit (20, 20)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:58 , ASN A:59 , GLU A:136 , GLN A:137 , ASP A:138 , TPO A:500	BINDING SITE FOR RESIDUE CA A 205
02	AC2	SOFTWARE	GLU A:136 , ASP A:138 , GLN A:148 , TPO A:500 , HOH A:2184 , HOH A:2192	BINDING SITE FOR RESIDUE CA A 206
03	AC3	SOFTWARE	GLN A:31 , ASN A:32 , GLU A:99 , SER A:101 , HOH A:2058 , HOH A:2150 , HOH A:2258	BINDING SITE FOR RESIDUE NAG A 207
04	AC4	SOFTWARE	ASP 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:2101 , HOH A:2106 , HOH A:2259 , HOH A:2260 , HOH A:2261	BINDING SITE FOR RESIDUE TPO A 500
05	AC5	SOFTWARE	GLU B:136 , ASP B:138 , GLN B:148 , TPO B:500 , HOH B:2186 , HOH B:2200	BINDING SITE FOR RESIDUE CA B 205
06	AC6	SOFTWARE	ASP B:58 , ASN B:59 , GLU B:136 , GLN B:137 , ASP B:138 , TPO B:500	BINDING SITE FOR RESIDUE CA B 206
07	AC7	SOFTWARE	GLN B:31 , ASN B:32 , GLU B:99 , HOH B:2059	BINDING SITE FOR RESIDUE NAG B 207
08	AC8	SOFTWARE	ASP B:58 , ASN B:59 , LEU B:62 , TYR B:74 , GLU B:136 , ASP B:138 , GLN B:148 , CA B:205 , CA B:206 , HOH B:2101 , HOH B:2267 , HOH B:2268 , HOH B:2269 , HOH B:2270	BINDING SITE FOR RESIDUE TPO B 500
09	AC9	SOFTWARE	ASP C:58 , ASN C:59 , GLU C:136 , GLN C:137 , ASP C:138 , TPO C:500	BINDING SITE FOR RESIDUE CA C 205
10	BC1	SOFTWARE	GLU C:136 , ASP C:138 , GLN C:148 , TPO C:500 , HOH C:2190 , HOH C:2199	BINDING SITE FOR RESIDUE CA C 206
11	BC2	SOFTWARE	GLN C:31 , ASN C:32 , GLU C:99 , HOH C:2214 , HOH C:2269	BINDING SITE FOR RESIDUE NAG C 207
12	BC3	SOFTWARE	ASP C:58 , ASN C:59 , LEU C:62 , TYR C:74 , GLU C:136 , ASP C:138 , GLN C:148 , CA C:205 , CA C:206 , HOH C:2101 , HOH C:2117 , HOH C:2271 , HOH C:2272 , HOH C:2273	BINDING SITE FOR RESIDUE TPO C 500
13	BC4	SOFTWARE	GLU D:136 , ASP D:138 , GLN D:148 , TPO D:500 , HOH D:2176 , HOH D:2190	BINDING SITE FOR RESIDUE CA D 205
14	BC5	SOFTWARE	ASP D:58 , ASN D:59 , GLU D:136 , GLN D:137 , ASP D:138 , TPO D:500	BINDING SITE FOR RESIDUE CA D 206
15	BC6	SOFTWARE	GLN D:31 , ASN D:32 , GLU D:99 , HOH D:2055 , HOH D:2140 , HOH D:2265	BINDING SITE FOR RESIDUE NAG D 207
16	BC7	SOFTWARE	ASP D:58 , ASN D:59 , LEU D:62 , TYR D:74 , GLU D:136 , ASP D:138 , GLN D:148 , CA D:205 , CA D:206 , HOH D:2266 , HOH D:2267	BINDING SITE FOR RESIDUE TPO D 500
17	BC8	SOFTWARE	ASP E:58 , ASN E:59 , GLU E:136 , GLN E:137 , ASP E:138 , TPO E:500	BINDING SITE FOR RESIDUE CA E 205
18	BC9	SOFTWARE	GLU E:136 , ASP E:138 , GLN E:148 , TPO E:500 , HOH E:2188 , HOH E:2201	BINDING SITE FOR RESIDUE CA E 206
19	CC1	SOFTWARE	GLN E:31 , ASN E:32 , GLU E:99 , HOH E:2056 , HOH E:2277 , HOH E:2278 , HOH E:2279	BINDING SITE FOR RESIDUE NAG E 207
20	CC2	SOFTWARE	ASP E:58 , ASN E:59 , LEU E:62 , TYR E:74 , GLU E:136 , ASP E:138 , GLN E:148 , CA E:205 , CA E:206 , HOH E:2097 , HOH E:2109 , HOH E:2128 , HOH E:2280 , HOH E:2281 , HOH E:2282	BINDING SITE FOR RESIDUE TPO E 500

Asymmetric/Biological Unit

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

Asymmetric/Biological Unit

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

Asymmetric/Biological Unit (3, 15)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_035814	G	141	S	SAMP_HUMAN	Unclassified	---	A/B/C/D/E	G	122	S
2	UniProt	VAR_006054	E	155	G	SAMP_HUMAN	Polymorphism	---	A/B/C/D/E	E	136	G
3	UniProt	VAR_006055	S	158	G	SAMP_HUMAN	Polymorphism	---	A/B/C/D/E	S	139	G

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

Asymmetric/Biological Unit (2, 10)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PTX_2	PS51828	Pentraxin (PTX) domain profile.	SAMP_HUMAN	24-223	5	A:5-204 B:5-204 C:5-204 D:5-204 E:5-204
2	PTX_1	PS00289	Pentraxin domain signature.	SAMP_HUMAN	112-119	5	A:93-100 B:93-100 C:93-100 D:93-100 E:93-100

Asymmetric/Biological Unit (2, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000255040	1	ENSE00000904938	chr1:159557615-159557775	161	SAMP_HUMAN	1-22	22	5	A:1-3 B:1-3 C:1-3 D:1-3 E:1-3	3 3 3 3 3
1.2	ENST00000255040	2	ENSE00000904939	chr1:159557891-159558655	765	SAMP_HUMAN	22-223	202	5	A:3-204 B:3-204 C:3-204 D:3-204 E:3-204	202 202 202 202 202

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 d2w08a_ A: Serum amyloid P component (SAP)                                                                                                                                                                   SCOP domains
               CATH domains 2w08A00 A:1-204  [code=2.60.120.200, no name defined]                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................eeee.........eeeeeeeee......eeeeeeee..eeeeeeeeeee..eeeeee..eeeeee........eeeeeeee....eeeeee..ee...ee...........eeee...........hhhhh..eeeeeeeee....hhhhhhhhhhh..............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)
                 2w08 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 d2w08b_ B: Serum amyloid P component (SAP)                                                                                                                                                                   SCOP domains
               CATH domains 2w08B00 B:1-204  [code=2.60.120.200, no name defined]                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................eeeee........eeeeeeeee......eeeeeeee..eeeeeeeeeee..eeeeee..eeeeee........eeeeeeee....eeeeee..ee...ee...........eeee...........hhhhh..eeeeeeeee....hhhhhhhhhhh.............eeeee........... 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)
                 2w08 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 d2w08c_ C: Serum amyloid P component (SAP)                                                                                                                                                                   SCOP domains
               CATH domains 2w08C00 C:1-204  [code=2.60.120.200, no name defined]                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................eeee.........eeeeeeeee......eeeeeeee..eeeeeeeeeee..eeeeee..eeeeee........eeeeeeee....eeeeee..ee...ee...........eeee...........hhhhh..eeeeeeeee....hhhhhhhhhh...............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)
                 2w08 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 d2w08d_ D: Serum amyloid P component (SAP)                                                                                                                                                                   SCOP domains
               CATH domains 2w08D00 D:1-204  [code=2.60.120.200, no name defined]                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee.......eeee........................eeeeeeee..eeeeeeeeeee..eeeeee..eeeeee....................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)
                 2w08 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 d2w08e_ E: Serum amyloid P component (SAP)                                                                                                                                                                   SCOP domains
               CATH domains 2w08E00 E:1-204  [code=2.60.120.200, no name defined]                                                                                                                                                        CATH domains
           Pfam domains (1) ------Pentaxin-2w08E01 E:7-200                                                                                                                                                                          ---- Pfam domains (1)
           Pfam domains (2) ------Pentaxin-2w08E02 E:7-200                                                                                                                                                                          ---- Pfam domains (2)
           Pfam domains (3) ------Pentaxin-2w08E03 E:7-200                                                                                                                                                                          ---- Pfam domains (3)
           Pfam domains (4) ------Pentaxin-2w08E04 E:7-200                                                                                                                                                                          ---- Pfam domains (4)
           Pfam domains (5) ------Pentaxin-2w08E05 E:7-200                                                                                                                                                                          ---- Pfam domains (5)
         Sec.struct. author ......eeeee.......eeee........................eeeeeeee..eeeeeeeeeee..eeeeee..eeeeee....................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: 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)
                 2w08 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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Concanavalin A-like lectins/glucanases (797)

Superfamily: Concanavalin A-like lectins/glucanases (797)

Family: Pentraxin (pentaxin) (18)

Protein domain: Serum amyloid P component (SAP) (12)

Human (Homo sapiens) [TaxId: 9606] (12)

1a	d2w08a_	A:
1b	d2w08b_	B:
1c	d2w08c_	C:
1d	d2w08d_	D:
1e	d2w08e_	E:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

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)

1a	2w08A00	A:1-204
1b	2w08B00	B:1-204
1c	2w08C00	C:1-204
1d	2w08D00	D:1-204
1e	2w08E00	E:1-204

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Concanavalin (293)

Family: Pentaxin (6)

Homo sapiens (Human) (6)

1a	Pentaxin-2w08E01	E:7-200
1b	Pentaxin-2w08E02	E:7-200
1c	Pentaxin-2w08E03	E:7-200
1d	Pentaxin-2w08E04	E:7-200
1e	Pentaxin-2w08E05	E:7-200

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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	2w08
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	SAMP_HUMAN \| P02743	:	1gyk 1lgn 1sac 2a3w 2a3x 2a3y 3d5o 3kqr 4avs 4avt 4avv 4ayu

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.

Description

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Ligands, Modified Residues, Ions (3, 20)

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SS Bonds (5, 5)

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