SMTL ID : 4avt.2 (1 other biounit)

Structure of CPHPC bound to Serum Amyloid P Component

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-pentamer

Ligands

10 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: D.58, N.59, E.136, Q.137, D.138 Ligands: GHE.3 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: 5 residues within 4Å: Chain A: E.136, D.138, D.145, Q.148 Ligands: GHE.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.136, A:D.138, A:D.138 CA.5: 5 residues within 4Å: Chain B: D.58, N.59, E.136, Q.137, D.138 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.6: 4 residues within 4Å: Chain B: E.136, D.138, D.145, Q.148 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.136, B:D.138, B:D.138 CA.8: 5 residues within 4Å: Chain C: D.58, N.59, E.136, Q.137, D.138 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.58, C:D.58, C:E.136, C:Q.137, C:D.138 CA.9: 3 residues within 4Å: Chain C: E.136, D.138, Q.148 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.136, C:D.138, C:D.138 CA.11: 5 residues within 4Å: Chain D: D.58, N.59, E.136, Q.137, D.138 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.12: 4 residues within 4Å: Chain D: E.136, D.138, D.145, Q.148 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.136, D:D.138, D:D.138 CA.14: 6 residues within 4Å: Chain E: D.58, N.59, E.136, Q.137, D.138 Ligands: GHE.16 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.15: 5 residues within 4Å: Chain E: E.136, D.138, D.145, Q.148 Ligands: GHE.16 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:E.136, E:D.138, E:D.138

2 x GHE: (2R)-1-[6-[(2R)-2-carboxypyrrolidin-1-yl]-6-oxidanylidene-hexanoyl]pyrrolidine-2-carboxylic acid(Non-covalent)

GHE.3: 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 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.62, A:Y.64 Hydrogen bonds: A:Q.148 GHE.16: 10 residues within 4Å: Chain E: D.58, N.59, L.62, Y.64, Y.74, E.136, D.138, Q.148 Ligands: CA.14, CA.15 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:L.62, E:Y.74 Hydrogen bonds: E:N.59, E:Q.148

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

NAG.4: 3 residues within 4Å: Chain A: Q.31, N.32, E.99 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.31, A:N.32 NAG.7: 5 residues within 4Å: Chain B: Q.31, N.32, E.99, S.101, D.161 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Q.31 Hydrogen bonds: B:Q.31, B:N.32, B:E.99, B:S.101 NAG.10: 4 residues within 4Å: Chain C: Q.31, N.32, E.99, D.161 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.31, C:N.32, C:E.99 NAG.13: 3 residues within 4Å: Chain D: Q.31, N.32, E.99 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.31, D:N.32 NAG.17: 3 residues within 4Å: Chain E: Q.31, N.32, E.99 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:Q.31, E:Q.31, E:N.32, E:E.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kolstoe, S.E. et al., Interaction of Serum Amyloid P Component with Hexanoyl Bis(D-Proline) (Cphpc). Acta Crystallogr.,Sect.D (2014)

Release Date

2013-06-19

Peptides

SERUM AMYLOID P-COMPONENT: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

C
F

D
H

E
J

SERUM AMYLOID P-COMPONENT

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