SMTL ID : 2a3x.1

Decameric crystal structure of human serum amyloid P-component bound to Bis-1,2-{[(Z)-2carboxy- 2-methyl-1,3-dioxane]- 5-yloxycarbonyl}-piperazine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-10-mer

Ligands

20 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.58, N.59, E.136, Q.137, D.138 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.58, A:D.58, A:E.136, A:Q.137, A:D.138 CA.2: 3 residues within 4Å: Chain A: E.136, D.138, Q.148 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.136, A:D.138 CA.3: 6 residues within 4Å: Chain B: D.58, N.59, E.136, Q.137, D.138 Ligands: CA.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.58, B:E.136, B:Q.137 CA.4: 5 residues within 4Å: Chain B: E.136, D.138, D.145, Q.148 Ligands: CA.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.136, B:D.138 CA.5: 7 residues within 4Å: Chain C: D.58, N.59, E.136, Q.137, D.138 Ligands: CA.6, CPK.22 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, CPK.22 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.136, C:D.138, C:D.138 CA.7: 6 residues within 4Å: Chain D: D.58, N.59, E.136, Q.137, D.138 Ligands: CPK.21 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.58, D:D.58, D:E.136, D:Q.137, D:D.138 CA.8: 5 residues within 4Å: Chain D: E.136, D.138, D.145, Q.148 Ligands: CPK.21 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.138, D:D.138 CA.9: 6 residues within 4Å: Chain E: D.58, N.59, E.136, Q.137, D.138 Ligands: CPK.23 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.58, E:D.58, E:E.136, E:Q.137, E:D.138 CA.10: 5 residues within 4Å: Chain E: E.136, D.138, D.145, Q.148 Ligands: CPK.23 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:E.136, E:D.138 CA.11: 4 residues within 4Å: Chain F: N.59, E.136, D.138, Q.148 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:E.136, F:D.138 CA.12: 5 residues within 4Å: Chain F: E.136, D.138, K.143, D.145, Q.148 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:E.136, F:E.136 CA.13: 6 residues within 4Å: Chain G: D.58, N.59, E.136, Q.137, D.138 Ligands: CA.14 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:E.136, G:E.136, G:Q.137, G:D.138 CA.14: 6 residues within 4Å: Chain G: E.136, Q.137, D.138, D.145, Q.148 Ligands: CA.13 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.136, G:D.138, G:D.145 CA.15: 7 residues within 4Å: Chain H: D.58, N.59, E.136, Q.137, D.138 Ligands: CA.16, CPK.23 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:D.58, H:E.136, H:E.136, H:Q.137, H:D.138 CA.16: 6 residues within 4Å: Chain H: E.136, D.138, D.145, Q.148 Ligands: CA.15, CPK.23 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:E.136, H:D.138 CA.17: 6 residues within 4Å: Chain I: D.58, N.59, E.136, Q.137, D.138 Ligands: CPK.21 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:D.58, I:D.58, I:E.136, I:E.136, I:D.138 CA.18: 4 residues within 4Å: Chain I: E.136, D.138, Q.148 Ligands: CPK.21 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:E.136, I:D.138, I:D.138 CA.19: 6 residues within 4Å: Chain J: D.58, N.59, E.136, Q.137, D.138 Ligands: CPK.22 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:D.58, J:E.136, J:E.136, J:Q.137 CA.20: 4 residues within 4Å: Chain J: E.136, D.138, Q.148 Ligands: CPK.22 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:E.136, J:D.138

3 x CPK: BIS-1,2-{[(Z)-2CARBOXY-2-METHYL-1,3-DIOXANE]-5-YLOXYCARBONYL}-PIPERAZINE(Non-covalent)

CPK.21: 19 residues within 4Å: Chain D: D.58, N.59, L.62, Y.64, Y.74, E.136, D.138, Q.148 Chain I: D.58, N.59, L.62, Y.74, E.136, D.138, Q.148 Ligands: CA.7, CA.8, CA.17, CA.18 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain I Hydrophobic interactions: D:L.62, I:L.62 Hydrogen bonds: D:N.59, D:N.59, D:Q.148, I:N.59 CPK.22: 20 residues within 4Å: Chain C: D.58, N.59, L.62, Y.64, Y.74, K.79, E.136, D.138, Q.148 Chain J: N.59, L.62, Y.64, Y.74, E.136, D.138, Q.148 Ligands: CA.5, CA.6, CA.19, CA.20 12 PLIP interactions: 8 interactions with chain C, 4 interactions with chain J Hydrophobic interactions: C:L.62, C:Y.64, C:E.136, J:L.62, J:Y.64, J:Y.74 Hydrogen bonds: C:N.59, C:N.59, C:Y.74, C:K.79, C:Q.148, J:N.59 CPK.23: 18 residues within 4Å: Chain E: D.58, N.59, L.62, Y.64, Y.74, E.136, D.138, Q.148 Chain H: N.59, L.62, Y.74, E.136, D.138, Q.148 Ligands: CA.9, CA.10, CA.15, CA.16 9 PLIP interactions: 6 interactions with chain E, 3 interactions with chain H Hydrophobic interactions: E:L.62, E:Y.64, E:E.136, H:L.62 Hydrogen bonds: E:N.59, E:N.59, E:Q.148, H:N.59, H: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: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

Serum amyloid P-component

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