2A3X: Serum amyloid P-component

Decameric crystal structure of human serum amyloid P-component bound to Bis-1,2-{[(Z)-2carboxy- 2-methyl-1,3-dioxane]- 5-yloxycarbonyl}-piperazine. Determined by X-ray diffraction at 3.0 Å resolution. Released 26 Jul 2005.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 10
Atoms: 16,606
Mol. weight: 235.01 kDa
Ligands: CA, CPK
Released: 26 Jul 2005

Explore 2A3X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2A3X contains 45 α-helices and 211 β-strands across 10 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 4 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	1
β-strand	7-11	5	2
β-strand	19-22	4	3
β-strand	30	1	4
β-strand	32-40	9	2
β-strand	47-54	8	3
β-strand	57-67	11	3
β-strand	70-75	6	3
β-strand	78-83	6	3
β-strand	92-99	8	2
β-strand	104-109	6	2
β-strand	112-113	2	2
α-helix	114-116	3
β-strand	117-118	2	2
β-strand	125	1	4
β-strand	130-133	4	3
α-helix	146-148	3
β-strand	152-160	9	2
α-helix	166-173	8
α-helix	177-180	4
β-strand	183	1	2
β-strand	188	1	1
β-strand	190-193	4	3
β-strand	197-200	4	2

Chain B: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	5
β-strand	7-11	5	6
β-strand	19-22	4	7
β-strand	30	1	8
β-strand	33-40	8	6
β-strand	47-54	8	7
β-strand	57-67	11	7
β-strand	70-75	6	7
β-strand	78-83	6	7
β-strand	92-98	7	6
β-strand	104-109	6	6
β-strand	112-113	2	6
α-helix	114-116	3
β-strand	117-118	2	6
α-helix	124	1
β-strand	125	1	8
α-helix	126	1
β-strand	130-133	4	7
α-helix	146-148	3
β-strand	152-160	9	6
α-helix	163-165	3
α-helix	166-174	9
β-strand	183	1	6
β-strand	188	1	5
β-strand	190-193	4	7
β-strand	197-200	4	6

Chain C: 3 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	9
β-strand	7-11	5	10
β-strand	19-22	4	11
β-strand	30	1	12
β-strand	32-40	9	10
β-strand	47-54	8	11
β-strand	57-67	11	11
β-strand	70-75	6	11
β-strand	78-83	6	11
β-strand	92-99	8	10
β-strand	104-109	6	10
β-strand	112-113	2	10
α-helix	114-116	3
β-strand	117-118	2	10
β-strand	125	1	12
β-strand	129-133	5	11
α-helix	146-148	3
β-strand	152-160	9	10
α-helix	166-173	8
β-strand	183-184	2	10
β-strand	187	1	10
β-strand	188	1	9
β-strand	190-193	4	11
β-strand	197-200	4	10

Chain D: 5 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	13
β-strand	7-11	5	14
β-strand	19-23	5	15
β-strand	30	1	16
β-strand	32-40	9	14
β-strand	47-54	8	15
β-strand	57-67	11	15
β-strand	70-75	6	15
β-strand	78-83	6	15
β-strand	92-99	8	14
β-strand	104-109	6	14
β-strand	113	1	14
α-helix	114-116	3
β-strand	117-118	2	14
β-strand	125	1	16
β-strand	130-133	4	15
α-helix	146-148	3
β-strand	152-160	9	14
α-helix	166-174	9
α-helix	177-180	4
β-strand	183	1	14
α-helix	185-187	3
β-strand	188	1	13
β-strand	189-193	5	15
β-strand	197-200	4	14

Chain E: 4 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	17
β-strand	7-11	5	18
β-strand	19-22	4	19
α-helix	23	1
β-strand	30	1	20
β-strand	32-40	9	18
β-strand	47-54	8	19
β-strand	57-67	11	19
β-strand	70-75	6	19
β-strand	78-83	6	19
β-strand	92-99	8	18
β-strand	104-109	6	18
β-strand	112-113	2	18
β-strand	117-118	2	18
β-strand	125	1	20
β-strand	130-133	4	19
β-strand	152-160	9	18
α-helix	163-165	3
α-helix	166-173	8
α-helix	177-180	4
β-strand	183-184	2	18
β-strand	188	1	17
β-strand	190-193	4	19
β-strand	197-200	4	18

Chain F: 4 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	7-10	4	21
β-strand	11	1	22
β-strand	19-22	4	23
β-strand	30	1	24
β-strand	33-40	8	21
β-strand	47-54	8	23
β-strand	57-67	11	23
β-strand	70-75	6	23
β-strand	78-83	6	23
β-strand	92-99	8	21
β-strand	104-107	4	21
β-strand	108-109	2	25
β-strand	112-113	2	25
β-strand	117-118	2	21
β-strand	125	1	24
β-strand	130-133	4	23
β-strand	137	1	26
β-strand	144	1	26
α-helix	146-148	3
β-strand	152	1	22
β-strand	153-160	8	21
α-helix	163-165	3
α-helix	166-174	9
α-helix	177-180	4
β-strand	183	1	21
β-strand	184	1	27
β-strand	187	1	27
β-strand	190-193	4	23
β-strand	197-200	4	21

Chain G: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	28
β-strand	7-11	5	29
β-strand	19-22	4	30
α-helix	29-30	2
β-strand	33-40	8	29
β-strand	47-54	8	30
β-strand	57-67	11	30
β-strand	70-75	6	30
β-strand	78-83	6	30
β-strand	92-98	7	29
β-strand	104-109	6	29
β-strand	112-113	2	29
α-helix	114-116	3
β-strand	117-118	2	29
β-strand	129-133	5	30
β-strand	139	1	31
β-strand	142	1	31
α-helix	146-148	3
β-strand	152-160	9	29
α-helix	166-173	8
α-helix	177-180	4
β-strand	183	1	29
β-strand	184	1	32
β-strand	187	1	32
β-strand	188	1	28
β-strand	190-193	4	30
β-strand	197-200	4	29

Chain H: 4 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	33
β-strand	7-11	5	34
β-strand	19-22	4	35
β-strand	30	1	36
β-strand	32-40	9	34
β-strand	47-50	4	37
β-strand	51-54	4	35
β-strand	57	1	35
β-strand	61-67	7	37
β-strand	70-75	6	37
β-strand	78-83	6	37
β-strand	92-99	8	34
β-strand	104-109	6	34
β-strand	112-113	2	34
α-helix	114-116	3
β-strand	117-118	2	34
β-strand	125	1	36
β-strand	129-133	5	35
α-helix	146-148	3
β-strand	152-160	9	34
α-helix	166-173	8
α-helix	177-179	3
β-strand	183-184	2	34
β-strand	187	1	34
β-strand	188	1	33
β-strand	190-193	4	35
β-strand	197-200	4	34

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serum amyloid P-component	A, B, C, D, E, F, G, H, I, J	protein	204	Homo sapiens	P02743 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H, I, J), FASTA

>2A3X_1 Serum amyloid P-component (chains A, B, C, D, E, F, G, H, I, J)
HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNE
LLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLR
QGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPA
NILDWQALNYEIRGYVIIKPLVWV

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	20
CPK	Bis-1,2-{[(Z)-2CARBOXY-2-methyl-1,3-dioxane]-5-yloxycarbonyl}-piperazine	C18 H26 N2 O12	3

Primary citation

Ligand-assisted Aggregation of Proteins: DIMERIZATION OF SERUM AMYLOID P COMPONENT BY BIVALENT LIGANDS. Ho, J.G., Kitov, P.I., Paszkiewicz, E. et al. J Biol Chem (2005) 280:31999-32008. DOI 10.1074/jbc.M504403200 · PubMed

Other PDB entries of the same protein (UniProt P02743 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4AVS 1.4 Å, Structure of N-Acetyl-L-Proline bound to Serum Amyloid P Component
3KQR 1.5 Å, The structure of serum amyloid p component bound to phosphoethanolamine
4AYU 1.5 Å, Structure of N-Acetyl-D-Proline bound to serum amyloid P component
4AVV 1.6 Å, Structure of CPHPC bound to Serum Amyloid P Component
2W08 1.7 Å, The structure of serum amyloid P component bound to 0-phospho- threonine
1SAC 2.0 Å, The structure of pentameric human serum amyloid P component
2A3Y 2.0 Å, Pentameric crystal structure of human serum amyloid P-component bound to…
1GYK 2.2 Å, Serum Amyloid P Component co-crystallised with MOBDG at neutral pH
2A3W 2.2 Å, Decameric structure of human serum amyloid P-component bound to…
1LGN 2.8 Å, Decameric damp complex of human serum amyloid P component
3D5O 2.8 Å, Structural recognition and functional activation of FcrR by innate pentraxins
4AVT 3.2 Å, Structure of CPHPC bound to Serum Amyloid P Component

Browse structure collections

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