SMTL ID : 4ayu.1

Structure of N-Acetyl-D-Proline bound to serum amyloid P component

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-pentamer

Ligands

10 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: E.136, D.138, Q.148 Ligands: CA.2, N8P.3 5 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: A:E.136, A:D.138, N8P.3, H2O.10, H2O.10 CA.2: 7 residues within 4Å: Chain A: D.58, N.59, E.136, Q.137, D.138 Ligands: CA.1, N8P.3 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.5: 5 residues within 4Å: Chain B: E.136, D.138, Q.148 Ligands: CA.6, N8P.7 5 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: B:E.136, B:D.138, N8P.7, H2O.21, H2O.21 CA.6: 7 residues within 4Å: Chain B: D.58, N.59, E.136, Q.137, D.138 Ligands: CA.5, N8P.7 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.9: 5 residues within 4Å: Chain C: E.136, D.138, Q.148 Ligands: CA.10, N8P.11 5 PLIP interactions: 2 interactions with chain C, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: C:E.136, C:D.138, N8P.11, H2O.31, H2O.31 CA.10: 7 residues within 4Å: Chain C: D.58, N.59, E.136, Q.137, D.138 Ligands: CA.9, N8P.11 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.15: 5 residues within 4Å: Chain D: E.136, D.138, Q.148 Ligands: CA.16, N8P.17 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.136, D:D.138, H2O.42, H2O.42, H2O.42 CA.16: 7 residues within 4Å: Chain D: D.58, N.59, E.136, Q.137, D.138 Ligands: CA.15, N8P.17 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.21: 5 residues within 4Å: Chain E: E.136, D.138, Q.148 Ligands: CA.22, N8P.23 5 PLIP interactions: 2 interactions with chain E, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: E:E.136, E:D.138, N8P.23, H2O.50, H2O.50 CA.22: 7 residues within 4Å: Chain E: D.58, N.59, E.136, Q.137, D.138 Ligands: CA.21, N8P.23 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

5 x N8P: N-ACETYL-D-PROLINE(Non-covalent)

N8P.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 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:Q.148 N8P.7: 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 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.62, B:Y.64, B:Y.74 Hydrogen bonds: B:N.59 N8P.11: 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 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:L.62, C:Y.64, C:Y.74, C:Y.74 Hydrogen bonds: C:N.59, C:N.59, C:Q.148 N8P.17: 10 residues within 4Å: Chain D: D.58, N.59, L.62, Y.64, Y.74, E.136, D.138, Q.148 Ligands: CA.15, CA.16 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:L.62, D:Y.64, D:Y.74 Hydrogen bonds: D:N.59, D:N.59, D:Q.148 N8P.23: 10 residues within 4Å: Chain E: D.58, N.59, L.62, Y.64, Y.74, E.136, D.138, Q.148 Ligands: CA.21, CA.22 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:L.62, E:Y.64, E:Y.74, E:Y.74 Hydrogen bonds: E:Q.148 Water bridges: E:Y.64

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

NAG.4: 4 residues within 4Å: Chain A: Q.31, N.32, E.99, S.101 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.31, A:N.32, A:S.101 Water bridges: A:E.99, A:E.99, A:E.99, A:S.101, A:S.101 NAG.8: 5 residues within 4Å: Chain B: Q.31, N.32, E.99, S.100, S.101 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.31, B:Q.31, B:N.32, B:S.101, B:S.101 Water bridges: B:E.99 NAG.12: 5 residues within 4Å: Chain C: Q.31, N.32, E.99, S.101 Ligands: GOL.13 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.31, C:N.32, C:S.101 Water bridges: C:E.99, C:E.99 NAG.18: 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.24: 5 residues within 4Å: Chain E: Q.31, N.32, E.99, V.163 Ligands: GOL.25 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.32 Water bridges: E:Q.31, E:V.163

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 7 residues within 4Å: Chain C: K.28, P.29, L.30, Q.31, N.32, D.161 Ligands: NAG.12 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.28, C:Q.31, C:Q.31, C:N.32, C:D.161 GOL.14: 5 residues within 4Å: Chain B: Y.40, P.91, W.203 Chain C: T.112, P.113 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Y.40, B:W.203, C:T.112 GOL.19: 7 residues within 4Å: Chain D: S.5, D.156, Y.158, G.175, P.177, W.185, Q.186 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.186 Water bridges: D:S.5, D:G.6, D:R.38, D:R.38 GOL.20: 3 residues within 4Å: Chain D: D.138, K.143, F.144 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.143, D:D.145 GOL.25: 7 residues within 4Å: Chain E: K.28, P.29, L.30, Q.31, N.32, D.161 Ligands: NAG.24 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:Q.31, E:N.32, E:D.161 Water bridges: E:N.32

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

2013-07-10

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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