SMTL ID : 4avs.1

Structure of N-Acetyl-L-Proline bound to Serum Amyloid P Component

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-pentamer

Ligands

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

NAG.1: 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.5: 5 residues within 4Å: Chain B: Q.31, N.32, E.99, S.162, V.163 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Q.31 Hydrogen bonds: B:N.32, B:V.163 NAG.9: 3 residues within 4Å: Chain C: Q.31, N.32, E.99 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.31 Water bridges: C:Q.31, C:N.32, C:N.32, C:E.99 NAG.13: 4 residues within 4Å: Chain D: Q.31, N.32, E.99, S.101 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.31, D:N.32 Water bridges: D:Q.31, D:E.99 NAG.17: 4 residues within 4Å: Chain E: Q.31, N.32, E.99, V.163 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:N.32, E:E.99, E:V.163 Water bridges: E:V.163

10 x CA: CALCIUM ION(Non-covalent)

CA.2: 7 residues within 4Å: Chain A: D.58, N.59, E.136, Q.137, D.138 Ligands: CA.3, N7P.4 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.3: 5 residues within 4Å: Chain A: E.136, D.138, Q.148 Ligands: CA.2, N7P.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, N7P.4, H2O.8, H2O.8 CA.6: 5 residues within 4Å: Chain B: E.136, D.138, Q.148 Ligands: CA.7, N7P.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, N7P.8, H2O.17, H2O.18 CA.7: 7 residues within 4Å: Chain B: D.58, N.59, E.136, Q.137, D.138 Ligands: CA.6, N7P.8 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.10: 7 residues within 4Å: Chain C: D.58, N.59, E.136, Q.137, D.138 Ligands: CA.11, N7P.12 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.11: 5 residues within 4Å: Chain C: E.136, D.138, Q.148 Ligands: CA.10, N7P.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, N7P.12, H2O.27, H2O.27 CA.14: 5 residues within 4Å: Chain D: E.136, D.138, Q.148 Ligands: CA.15, N7P.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.37, H2O.37 CA.15: 7 residues within 4Å: Chain D: D.58, N.59, E.136, Q.137, D.138 Ligands: CA.14, N7P.16 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.18: 7 residues within 4Å: Chain E: D.58, N.59, E.136, Q.137, D.138 Ligands: CA.19, N7P.20 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.19: 5 residues within 4Å: Chain E: E.136, D.138, Q.148 Ligands: CA.18, N7P.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, N7P.20, H2O.47, H2O.47

5 x N7P: 1-ACETYL-L-PROLINE(Non-covalent)

N7P.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.2, CA.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.62, A:Y.64, A:Y.74 Hydrogen bonds: A:N.59, A:N.59 N7P.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.6, CA.7 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.62, B:Y.64, B:Y.64, B:Y.74 Hydrogen bonds: B:N.59, B:N.59, B:Q.148 N7P.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.10, CA.11 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.62, C:Y.64 Hydrogen bonds: C:N.59, C:N.59, C:Q.148 Water bridges: C:R.77 N7P.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.14, CA.15 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:L.62, D:Y.64, D:Y.64, D:Y.74 Hydrogen bonds: D:N.59, D:N.59, D:Q.148 Water bridges: D:Y.74 N7P.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.18, CA.19 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:L.62, E:Y.64, E:Y.74 Hydrogen bonds: E:N.59, E:N.59, E:Q.148

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
A

B
B

C
C

D
D

E
E

SERUM AMYLOID P-COMPONENT

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