2A3Y: Serum amyloid P-component

Pentameric crystal structure of human serum amyloid P-component bound to Bis-1,2-{[(Z)-2carboxy-2-methyl-1,3-dioxane]-5-yloxycarbamoyl}-ethane. Determined by X-ray diffraction at 2.0 Å resolution. Released 26 Jul 2005.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 5
Atoms: 8,798
Mol. weight: 118.99 kDa
Ligands: CA, CPJ
Released: 26 Jul 2005

Explore 2A3Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2A3Y contains 26 α-helices and 100 β-strands across 5 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: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	1
β-strand	7-11	5	2
β-strand	19-23	5	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
α-helix	126	1
β-strand	130-133	4	3
α-helix	146-148	3
β-strand	152-160	9	2
α-helix	163-165	3
α-helix	166-174	9
α-helix	177-179	3
β-strand	183-184	2	2
β-strand	188	1	1
β-strand	189-193	5	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
α-helix	29	1
β-strand	30	1	8
β-strand	32-40	9	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	92-99	8	6
β-strand	104-109	6	6
β-strand	112-113	2	6
α-helix	114-116	3
β-strand	117-118	2	6
β-strand	125	1	8
β-strand	130-133	4	7
α-helix	146-148	3
β-strand	152-160	9	6
α-helix	163-165	3
α-helix	166-173	8
α-helix	177-179	3
β-strand	183-184	2	6
β-strand	188	1	5
β-strand	190-193	4	7
β-strand	197-200	4	6

Chain C: 5 helices, 20 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
β-strand	117-118	2	10
β-strand	125	1	12
β-strand	130-133	4	11
α-helix	146-148	3
β-strand	152-160	9	10
α-helix	163-165	3
α-helix	166-173	8
α-helix	177-179	3
β-strand	183-184	2	10
α-helix	185-187	3
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	19-22	4	15
α-helix	23	1
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	112-113	2	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	166-173	8
α-helix	177-179	3
β-strand	183-184	2	14
β-strand	188	1	13
β-strand	190-193	4	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	19-23	5	19
α-helix	29	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
α-helix	146-148	3
β-strand	152-160	9	18
α-helix	166-174	9
α-helix	177-179	3
β-strand	183-184	2	18
β-strand	188	1	17
β-strand	189-193	5	19
β-strand	197-200	4	18

Molecules and chains

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

Sequence of entity 1 (A, B, C, D, E), FASTA

>2A3Y_1 Serum amyloid P-component (chains A, B, C, D, E)
HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNE
LLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLR
QGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPA
NILDWQALNYEIRGYVIIKPLVWV

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	10
CPJ	Bis-1,2-{[(Z)-2-carboxy-2-methyl-1,3-dioxane]-5-yloxycarbamoyl}-ethane	C16 H24 N2 O12	5

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
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
2A3X 3.0 Å, Decameric crystal structure of human serum amyloid P-component bound to…
4AVT 3.2 Å, Structure of CPHPC bound to Serum Amyloid P Component

Browse structure collections

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