3KQR: Serum amyloid p component

The structure of serum amyloid p component bound to phosphoethanolamine. Determined by X-ray diffraction at 1.5 Å resolution. Released 8 Dec 2010.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Homo sapiens
Chains: 5
Atoms: 10,096
Mol. weight: 118.62 kDa
Ligands: OPE, CA, NAG
Released: 8 Dec 2010

Explore 3KQR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3KQR contains 24 α-helices and 98 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: 5 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	7-11	5	1
β-strand	19-23	5	2
α-helix	29	1
β-strand	30	1	3
β-strand	32-40	9	1
β-strand	47-54	8	2
β-strand	57-67	11	2
β-strand	70-75	6	2
β-strand	78-83	6	2
β-strand	92-99	8	1
β-strand	104-109	6	1
β-strand	112-113	2	1
α-helix	114-116	3
β-strand	117-118	2	1
β-strand	125	1	3
β-strand	130-133	4	2
α-helix	146-148	3
β-strand	152-160	9	1
α-helix	166-174	9
α-helix	177-179	3
β-strand	183-184	2	1
β-strand	189-193	5	2
β-strand	197-200	4	1

Chain B: 5 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	4
β-strand	7-11	5	5
β-strand	19-23	5	6
β-strand	30	1	7
β-strand	32-40	9	5
β-strand	47-54	8	6
β-strand	57-67	11	6
β-strand	70-75	6	6
β-strand	78-83	6	6
β-strand	92-99	8	5
β-strand	104-109	6	5
β-strand	112-113	2	5
α-helix	114-116	3
β-strand	117-118	2	5
β-strand	125	1	7
α-helix	126	1
β-strand	130-133	4	6
α-helix	146-148	3
β-strand	152-160	9	5
α-helix	166-174	9
α-helix	177-179	3
β-strand	183-184	2	5
β-strand	188	1	4
β-strand	189-193	5	6
β-strand	197-200	4	5

Chain C: 4 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	8
β-strand	7-11	5	9
β-strand	19-22	4	10
β-strand	30	1	11
β-strand	32-40	9	9
β-strand	47-54	8	10
β-strand	57-67	11	10
β-strand	70-75	6	10
β-strand	78-83	6	10
β-strand	92-99	8	9
β-strand	104-109	6	9
β-strand	112-113	2	9
α-helix	114-116	3
β-strand	117-118	2	9
β-strand	125	1	11
β-strand	130-133	4	10
α-helix	146-148	3
β-strand	152-160	9	9
α-helix	166-173	8
α-helix	177-179	3
β-strand	183-184	2	9
β-strand	188	1	8
β-strand	190-193	4	10
β-strand	197-200	4	9

Chain D: 5 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	12
β-strand	7-11	5	13
β-strand	19-22	4	14
α-helix	29	1
β-strand	30	1	15
β-strand	32-40	9	13
β-strand	47-54	8	14
β-strand	57-67	11	14
β-strand	70-75	6	14
β-strand	78-83	6	14
β-strand	92-99	8	13
β-strand	104-109	6	13
β-strand	112-113	2	13
α-helix	114-116	3
β-strand	117-118	2	13
β-strand	125	1	15
β-strand	130-133	4	14
α-helix	146-148	3
β-strand	152-160	9	13
α-helix	166-174	9
α-helix	177-179	3
β-strand	183-184	2	13
β-strand	188	1	12
β-strand	190-193	4	14
β-strand	197-200	4	13

Chain E: 5 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	16
β-strand	7-11	5	17
β-strand	19-23	5	18
α-helix	29	1
β-strand	30	1	19
β-strand	32-40	9	17
β-strand	47-54	8	18
β-strand	57-67	11	18
β-strand	70-75	6	18
β-strand	78-83	6	18
β-strand	92-99	8	17
β-strand	104-109	6	17
β-strand	112-113	2	17
α-helix	114-116	3
β-strand	117-118	2	17
β-strand	125	1	19
β-strand	130-133	4	18
α-helix	146-148	3
β-strand	152-160	9	17
α-helix	166-174	9
α-helix	176-179	4
β-strand	183-184	2	17
β-strand	188	1	16
β-strand	189-193	5	18
β-strand	197-200	4	17

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

>3KQR_1 Serum amyloid P-component (chains A, B, C, D, E)
HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNE
LLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLR
QGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPA
NILDWQALNYEIRGYVIIKPLVWV

Ligands and cofactors

ID	Name	Formula	Copies
OPE	Phosphoric acid mono-(2-amino-ethyl) ester	C2 H8 N O4 P	5
CA	Calcium ion	Ca	10
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5

Primary citation

Structural basis of ligand specificity in the human pentraxins, C-reactive protein and serum amyloid P component. Mikolajek, H., Kolstoe, S.E., Pye, V.E. et al. J Mol Recognit (2011) 24:371-377. DOI 10.1002/jmr.1090 · 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
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
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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