1LGN: Serum amyloid P component

Decameric damp complex of human serum amyloid P component. Determined by X-ray diffraction at 2.8 Å resolution. Released 24 Dec 1997.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 5
Atoms: 8,365
Mol. weight: 118.47 kDa
Ligands: D5M, CA
Released: 24 Dec 1997

Explore 1LGN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1LGN contains 22 α-helices and 102 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: 4 helices, 21 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	104-105	2	5
β-strand	106-109	4	2
β-strand	112-113	2	2
β-strand	117-118	2	5
β-strand	125	1	4
β-strand	129-133	5	3
α-helix	146-148	3
β-strand	152-160	9	2
α-helix	166-174	9
α-helix	177-180	4
β-strand	183-184	2	2
α-helix	185-187	3
β-strand	188	1	1
β-strand	190-193	4	3
β-strand	197-200	4	2

Chain B: 5 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	6
β-strand	7-11	5	7
β-strand	19-22	4	8
β-strand	30	1	9
β-strand	32-40	9	7
β-strand	47-54	8	8
β-strand	57-67	11	8
β-strand	70-75	6	8
β-strand	78-83	6	8
β-strand	92-99	8	7
β-strand	104-109	6	7
β-strand	112-113	2	7
α-helix	114-116	3
β-strand	117-118	2	7
β-strand	125	1	9
β-strand	130-133	4	8
α-helix	146-148	3
β-strand	152-160	9	7
α-helix	166-174	9
α-helix	177-180	4
β-strand	183-184	2	7
α-helix	185-187	3
β-strand	188	1	6
β-strand	190-193	4	8
β-strand	197-200	4	7

Chain C: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	10
β-strand	7-11	5	11
β-strand	19-22	4	12
β-strand	30	1	13
β-strand	32-40	9	11
β-strand	47-54	8	12
β-strand	57-67	11	12
β-strand	70-75	6	12
β-strand	78-83	6	12
β-strand	92-99	8	11
β-strand	104-107	4	11
β-strand	108-109	2	14
β-strand	112-113	2	14
α-helix	114-116	3
β-strand	117-118	2	11
β-strand	125	1	13
β-strand	130-133	4	12
α-helix	146-148	3
β-strand	152-160	9	11
α-helix	166-173	8
α-helix	177-180	4
β-strand	183-184	2	11
α-helix	185-187	3
β-strand	188	1	10
β-strand	190-193	4	12
β-strand	197-200	4	11

Chains D and E: 4 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	15
β-strand	7-11	5	16
β-strand	19-22	4	17
β-strand	30	1	18
β-strand	32-40	9	16
β-strand	47-54	8	17
β-strand	57-67	11	17
β-strand	70-75	6	17
β-strand	78-83	6	17
β-strand	92-99	8	16
β-strand	104-109	6	16
β-strand	112-113	2	16
β-strand	117-118	2	16
β-strand	125	1	18
β-strand	130-133	4	17
α-helix	146-148	3
β-strand	152-160	9	16
α-helix	166-174	9
α-helix	177-180	4
β-strand	183-184	2	16
α-helix	185-187	3
β-strand	188	1	15
β-strand	190-193	4	17
β-strand	197-200	4	16

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

>1LGN_1 SERUM AMYLOID P COMPONENT (chains A, B, C, D, E)
HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNE
LLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLR
QGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPA
NILDWQALNYEIRGYVIIKPLVWV

Ligands and cofactors

ID	Name	Formula	Copies
D5M	2'-deoxyadenosine-5'-monophosphate	C10 H14 N5 O6 P	5
CA	Calcium ion	Ca	10

Primary citation

Crystal structure of a decameric complex of human serum amyloid P component with bound dAMP. Hohenester, E., Hutchinson, W.L., Pepys, M.B. et al. J Mol Biol (1997) 269:570-578. DOI 10.1006/jmbi.1997.1075 · 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…
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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