1GYK: Serum amyloid P-component

Serum Amyloid P Component co-crystallised with MOBDG at neutral pH. Determined by X-ray diffraction at 2.2 Å resolution. Released 22 May 2003.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: HOMO SAPIENS
Chains: 5
Atoms: 8,326
Mol. weight: 117.83 kDa
Ligands: CDG, CA
Released: 22 May 2003

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

Secondary structure: helices and β-sheets

1GYK contains 20 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.

Chains A, B, C and D: 4 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	1
β-strand	7-11	5	2
β-strand	20-22	3	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	190-192	3	3
β-strand	197-200	4	2

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	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
α-helix	114-116	3
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	166-174	9
α-helix	177-180	4
β-strand	183	1	18
β-strand	188	1	17
β-strand	190-193	4	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

>1GYK_1 SERUM AMYLOID P-COMPONENT (chains A, B, C, D, E)
HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNE
LLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLR
QGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPA
NILDWQALNYEIRGYVIIKPLVWV

Ligands and cofactors

ID	Name	Formula	Copies
CDG	Methyl 4,6-O-[(1R)-1-carboxyethylidene]-beta-D-galactopyranoside	C10 H16 O8	4
CA	Calcium ion	Ca	9

Primary citation

The Structures of Crystalline Complexes of Human Serum Amyloid P Component with its Carbohydrate Ligand, the Cyclic Pyruvate Acetal of Galactose. Thompson, D., Pepys, M.B., Tickle, I. et al. J Mol Biol (2002) 320:1081. DOI 10.1016/S0022-2836(02)00514-4 · 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…
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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