SMTL ID : 2w08.1

The structure of serum amyloid P component bound to 0-phospho- threonine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 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, TPO.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.58, A:E.136, A:Q.137, A:D.138, TPO.4 CA.2: 5 residues within 4Å: Chain A: E.136, D.138, Q.148 Ligands: CA.1, TPO.4 5 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: A:E.136, A:D.138, TPO.4, H2O.8, H2O.8 CA.5: 5 residues within 4Å: Chain B: E.136, D.138, Q.148 Ligands: CA.6, TPO.8 5 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: B:E.136, B:D.138, TPO.8, H2O.18, H2O.18 CA.6: 7 residues within 4Å: Chain B: D.58, N.59, E.136, Q.137, D.138 Ligands: CA.5, TPO.8 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.58, B:E.136, B:Q.137, B:D.138, TPO.8 CA.9: 7 residues within 4Å: Chain C: D.58, N.59, E.136, Q.137, D.138 Ligands: CA.10, TPO.12 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:D.58, C:E.136, C:Q.137, C:D.138, TPO.12 CA.10: 5 residues within 4Å: Chain C: E.136, D.138, Q.148 Ligands: CA.9, TPO.12 5 PLIP interactions: 2 interactions with chain C, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: C:E.136, C:D.138, TPO.12, H2O.28, H2O.29 CA.13: 5 residues within 4Å: Chain D: E.136, D.138, Q.148 Ligands: CA.14, TPO.16 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.136, D:D.138, D:D.138, H2O.38, H2O.39 CA.14: 7 residues within 4Å: Chain D: D.58, N.59, E.136, Q.137, D.138 Ligands: CA.13, TPO.16 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.17: 7 residues within 4Å: Chain E: D.58, N.59, E.136, Q.137, D.138 Ligands: CA.18, TPO.20 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Ligand interactions Metal complexes: E:E.136, E:E.136, E:Q.137, E:D.138, TPO.20 CA.18: 5 residues within 4Å: Chain E: E.136, D.138, Q.148 Ligands: CA.17, TPO.20 5 PLIP interactions: 2 interactions with chain E, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: E:E.136, E:D.138, TPO.20, H2O.49, H2O.49

5 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 4 residues within 4Å: Chain A: Q.31, N.32, E.99, S.101 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.32, A:E.99, A:S.101 NAG.7: 3 residues within 4Å: Chain B: Q.31, N.32, E.99 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.31 Water bridges: B:Q.31, B:E.99, B:S.101 NAG.11: 3 residues within 4Å: Chain C: Q.31, N.32, E.99 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Q.31 Water bridges: C:Q.31, C:Q.31, C:N.32, C:N.32, C:E.99, C:E.99 NAG.15: 3 residues within 4Å: Chain D: Q.31, N.32, E.99 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.31, D:N.32 Water bridges: D:E.99 NAG.19: 3 residues within 4Å: Chain E: Q.31, N.32, E.99 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:N.32, E:E.99, E:S.101 Water bridges: E:Q.31, E:Q.31, E:Q.31, E:V.163

5 x TPO: PHOSPHOTHREONINE(Non-functional Binders)

TPO.4: 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 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.62 Hydrogen bonds: A:N.59, A:Y.64, A:Y.64, A:E.66, A:Y.74, A:Q.148 Water bridges: A:N.59, A:K.79, A:K.79 TPO.8: 10 residues within 4Å: Chain B: 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 B Hydrophobic interactions: B:L.62 Hydrogen bonds: B:N.59, B:Y.64, B:Y.74, B:Q.148 TPO.12: 10 residues within 4Å: Chain C: D.58, N.59, L.62, Y.64, Y.74, E.136, D.138, Q.148 Ligands: CA.9, CA.10 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:L.62 Hydrogen bonds: C:N.59, C:Y.64, C:Y.74, C:Y.74, C:Q.148, C:Q.148 Water bridges: C:D.58, C:R.77 TPO.16: 10 residues within 4Å: Chain D: D.58, N.59, L.62, Y.64, Y.74, E.136, D.138, Q.148 Ligands: CA.13, CA.14 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:L.62 Hydrogen bonds: D:N.59, D:Y.64, D:Y.74, D:Y.74, D:Q.148, D:Q.148 Water bridges: D:D.58 TPO.20: 10 residues within 4Å: Chain E: D.58, N.59, L.62, Y.64, Y.74, E.136, D.138, Q.148 Ligands: CA.17, CA.18 12 PLIP interactions: 12 interactions with chain E Hydrophobic interactions: E:L.62 Hydrogen bonds: E:Y.64, E:Y.64, E:Y.74, E:Y.74, E:Q.148 Water bridges: E:N.59, E:N.59, E:N.59, E:E.66, E:K.79, E:K.79

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kolstoe, S.E. et al., Molecular Dissection of Alzheimer'S Disease Neuropathology by Depletion of Serum Amyloid P Component. Proc.Natl.Acad.Sci.USA (2009)

Release Date

2009-04-14

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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