SMTL ID : 2a3w.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-10-mer

Ligands

20 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.16 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.16 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.136, A:D.138, A:D.138, H2O.1, H2O.18 CA.3: 5 residues within 4Å: Chain B: E.136, D.138, Q.148 Ligands: CA.4, CPJ.5 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.136, B:D.138, B:D.138, H2O.3, H2O.3 CA.4: 7 residues within 4Å: Chain B: D.58, N.59, E.136, Q.137, D.138 Ligands: CA.3, CPJ.5 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.58, B:E.136, B:E.136, B:Q.137, B:D.138 CA.6: 7 residues within 4Å: Chain C: D.58, N.59, E.136, Q.137, D.138 Ligands: CA.7, CPJ.8 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.7: 5 residues within 4Å: Chain C: E.136, D.138, Q.148 Ligands: CA.6, CPJ.8 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.136, C:D.138, C:D.138, H2O.8, H2O.8 CA.9: 7 residues within 4Å: Chain D: D.58, N.59, E.136, Q.137, D.138 Ligands: CA.10, CPJ.11 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.58, D:D.58, D:E.136, D:E.136, D:D.138 CA.10: 5 residues within 4Å: Chain D: E.136, D.138, Q.148 Ligands: CA.9, CPJ.11 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.136, D:D.138, D:D.138, H2O.12, H2O.12 CA.12: 7 residues within 4Å: Chain E: D.58, N.59, E.136, Q.137, D.138 Ligands: CA.13, CPJ.19 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.13: 5 residues within 4Å: Chain E: E.136, D.138, Q.148 Ligands: CA.12, CPJ.19 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.136, E:D.138, E:D.138, H2O.15, H2O.15 CA.14: 7 residues within 4Å: Chain F: D.58, N.59, E.136, Q.137, D.138 Ligands: CA.15, CPJ.16 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.58, F:E.136, F:E.136, F:Q.137, F:D.138 CA.15: 5 residues within 4Å: Chain F: E.136, D.138, Q.148 Ligands: CA.14, CPJ.16 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.136, F:D.138, F:D.138, H2O.19, H2O.19 CA.17: 7 residues within 4Å: Chain G: D.58, N.59, E.136, Q.137, D.138 Ligands: CA.18, CPJ.19 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:D.58, G:D.58, G:E.136, G:E.136, G:D.138 CA.18: 5 residues within 4Å: Chain G: E.136, D.138, Q.148 Ligands: CA.17, CPJ.19 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.136, G:D.138, G:D.138, H2O.22, H2O.22 CA.20: 7 residues within 4Å: Chain H: D.58, N.59, E.136, Q.137, D.138 Ligands: CPJ.11, CA.21 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.21: 5 residues within 4Å: Chain H: E.136, D.138, Q.148 Ligands: CPJ.11, CA.20 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:E.136, H:D.138, H:D.138, H2O.26 CA.22: 7 residues within 4Å: Chain I: D.58, N.59, E.136, Q.137, D.138 Ligands: CPJ.8, CA.23 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:D.58, I:E.136, I:E.136, I:Q.137, I:D.138 CA.23: 5 residues within 4Å: Chain I: E.136, D.138, Q.148 Ligands: CPJ.8, CA.22 5 PLIP interactions: 3 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:E.136, I:D.138, I:D.138, H2O.29, H2O.29 CA.24: 7 residues within 4Å: Chain J: D.58, N.59, E.136, Q.137, D.138 Ligands: CPJ.5, CA.25 5 PLIP interactions: 5 interactions with chain J Metal complexes: J:D.58, J:E.136, J:E.136, J:Q.137, J:D.138 CA.25: 5 residues within 4Å: Chain J: E.136, D.138, Q.148 Ligands: CPJ.5, CA.24 5 PLIP interactions: 3 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:E.136, J:D.138, J:D.138, H2O.33, H2O.33

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

CPJ.5: 18 residues within 4Å: Chain B: D.58, N.59, L.62, Y.74, E.136, D.138, Q.148 Chain J: D.58, N.59, L.62, Y.74, E.136, D.138, Q.148 Ligands: CA.3, CA.4, CA.24, CA.25 6 PLIP interactions: 4 interactions with chain J, 2 interactions with chain B Hydrophobic interactions: J:L.62, B:L.62 Hydrogen bonds: J:N.59, J:N.59, J:Q.148, B:Q.148 CPJ.8: 20 residues within 4Å: Chain C: 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.64, Y.74, E.136, D.138, Q.148 Ligands: CA.6, CA.7, CA.22, CA.23 9 PLIP interactions: 4 interactions with chain C, 5 interactions with chain I Hydrophobic interactions: C:L.62, I:L.62, I:Y.64 Hydrogen bonds: C:N.59, C:Q.148, I:N.59, I:N.59, I:Q.148 Water bridges: C:Y.74 CPJ.11: 20 residues within 4Å: Chain D: D.58, N.59, L.62, Y.64, Y.74, E.136, D.138, Q.148 Chain H: D.58, N.59, L.62, Y.64, Y.74, E.136, D.138, Q.148 Ligands: CA.9, CA.10, CA.20, CA.21 8 PLIP interactions: 3 interactions with chain D, 5 interactions with chain H Hydrophobic interactions: D:L.62, H:L.62, H:Y.64 Hydrogen bonds: D:N.59, D:Q.148, H:N.59, H:N.59, H:Q.148 CPJ.16: 18 residues within 4Å: Chain A: D.58, N.59, L.62, Y.74, E.136, D.138, Q.148 Chain F: D.58, N.59, L.62, Y.74, E.136, D.138, Q.148 Ligands: CA.1, CA.2, CA.14, CA.15 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain F Hydrophobic interactions: A:L.62, F:L.62 Hydrogen bonds: A:N.59, A:Q.148, A:Q.148, F:N.59, F:N.59, F:Q.148 Water bridges: A:Y.74 CPJ.19: 19 residues within 4Å: Chain E: D.58, N.59, L.62, Y.74, E.136, D.138, Q.148 Chain G: D.58, N.59, L.62, Y.64, Y.74, E.136, D.138, Q.148 Ligands: CA.12, CA.13, CA.17, CA.18 8 PLIP interactions: 5 interactions with chain E, 3 interactions with chain G Hydrophobic interactions: E:L.62, G:L.62 Hydrogen bonds: E:N.59, E:Q.148, E:Q.148, G:N.59, G:Q.148 Water bridges: E:D.58

Links

RCSB   PDBe   PDBe-KB   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
K

B
L

C
M

D
N

E
O

F
P

G
Q

H
R

I
S

J
T

Serum amyloid P-component

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