SMTL ID : 2a3y.1

Pentameric crystal structure of human serum amyloid P-component bound to Bis-1,2-{[(Z)-2carboxy-2-methyl-1,3-dioxane]-5-yloxycarbamoyl}-ethane.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-pentamer

Ligands

10 x CA: CALCIUM ION(Non-covalent)

CA.1: 7 residues within 4Å: Chain A: D.58, N.59, E.136, Q.137, D.138 Ligands: CA.2, CPJ.11 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.58, A:E.136, A:E.136, A:Q.137, A:D.138 CA.2: 5 residues within 4Å: Chain A: E.136, D.138, Q.148 Ligands: CA.1, CPJ.11 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.136, A:D.138, A:D.138, H2O.77, H2O.78 CA.3: 7 residues within 4Å: Chain B: D.58, N.59, E.136, Q.137, D.138 Ligands: CA.4, CPJ.12 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.58, B:D.58, B:E.136, B:Q.137, B:D.138 CA.4: 5 residues within 4Å: Chain B: E.136, D.138, Q.148 Ligands: CA.3, CPJ.12 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.136, B:D.138, B:D.138, H2O.124, H2O.125 CA.5: 7 residues within 4Å: Chain C: D.58, N.59, E.136, Q.137, D.138 Ligands: CA.6, CPJ.13 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.58, C:E.136, C:E.136, C:Q.137, C:D.138 CA.6: 5 residues within 4Å: Chain C: E.136, D.138, Q.148 Ligands: CA.5, CPJ.13 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.136, C:D.138, C:D.138, H2O.225, H2O.226 CA.7: 7 residues within 4Å: Chain D: D.58, N.59, E.136, Q.137, D.138 Ligands: CA.8, CPJ.15 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.58, D:E.136, D:E.136, D:Q.137, D:D.138 CA.8: 5 residues within 4Å: Chain D: E.136, D.138, Q.148 Ligands: CA.7, CPJ.15 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.136, D:D.138, D:D.138, H2O.371, H2O.372 CA.9: 7 residues within 4Å: Chain E: D.58, N.59, E.136, Q.137, D.138 Ligands: CA.10, CPJ.14 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.58, E:E.136, E:E.136, E:Q.137, E:D.138 CA.10: 5 residues within 4Å: Chain E: E.136, D.138, Q.148 Ligands: CA.9, CPJ.14 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.136, E:D.138, E:D.138, H2O.471, H2O.472

5 x CPJ: BIS-1,2-{[(Z)-2-CARBOXY-2-METHYL-1,3-DIOXANE]-5-YLOXYCARBAMOYL}-ETHANE(Non-covalent)

CPJ.11: 10 residues within 4Å: Chain A: D.58, N.59, L.62, Y.64, Y.74, E.136, D.138, Q.148 Ligands: CA.1, CA.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.62, A:Y.64 Hydrogen bonds: A:N.59, A:Q.148 CPJ.12: 11 residues within 4Å: Chain B: D.58, N.59, L.62, Y.64, Y.74, R.77, E.136, D.138, Q.148 Ligands: CA.3, CA.4 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.62, B:Y.64 Hydrogen bonds: B:N.59, B:N.59, B:Y.74, B:Q.148 CPJ.13: 10 residues within 4Å: Chain C: D.58, N.59, L.62, Y.64, Y.74, E.136, D.138, Q.148 Ligands: CA.5, CA.6 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.62, C:Y.64 Hydrogen bonds: C:N.59, C:Y.74, C:Q.148 CPJ.14: 10 residues within 4Å: Chain E: D.58, N.59, L.62, Y.64, Y.74, E.136, D.138, Q.148 Ligands: CA.9, CA.10 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:L.62, E:Y.64 Hydrogen bonds: E:N.59, E:N.59, E:Q.148 CPJ.15: 10 residues within 4Å: Chain D: D.58, N.59, L.62, Y.64, Y.74, E.136, D.138, Q.148 Ligands: CA.7, CA.8 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.62, D:Y.64 Hydrogen bonds: D:N.59, D:N.59, D:Q.148

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Ho, J.G. et al., Ligand-assisted Aggregation of Proteins: DIMERIZATION OF SERUM AMYLOID P COMPONENT BY BIVALENT LIGANDS. J.Biol.Chem. (2005)

Release Date

2005-07-26

Peptides

Serum amyloid P-component: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Serum amyloid P-component

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