SMTL ID : 4avv.1

Structure of CPHPC bound to Serum Amyloid P Component

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-pentamer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 4 residues within 4Å: Chain B: Q.31, N.32, E.99, S.101 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- NAG- GAL- SIA- MAN- NAG- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-NAG-GAL-SIA-MAN-NAG-GAL-SIA.2: 8 residues within 4Å: Chain D: Q.31, N.32, E.99, S.101 Chain E: Y.190, E.191, I.192, R.193 11 PLIP interactions: 1 interactions with chain D, 10 interactions with chain E Water bridges: D:S.101, E:T.2, E:Y.190, E:E.191, E:I.192 Hydrogen bonds: E:Y.190, E:Y.190, E:E.191, E:I.192, E:R.193, E:R.193

8 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 4 residues within 4Å: Chain A: R.120 Ligands: ACT.4, ACT.6, CD.10 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.120 ACT.4: 4 residues within 4Å: Chain A: R.57 Ligands: ACT.3, CD.10, ACT.13 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.57 Salt bridges: A:R.57 ACT.6: 6 residues within 4Å: Chain A: R.77, H.78, R.120 Ligands: ACT.3, CD.10, ACT.13 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.77, A:H.78, A:R.120 ACT.13: 4 residues within 4Å: Chain A: R.77 Ligands: ACT.4, ACT.6, CD.10 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.77 ACT.18: 3 residues within 4Å: Chain B: H.78, R.120 Ligands: CD.22 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.57 Salt bridges: B:H.78, B:R.120 ACT.41: 4 residues within 4Å: Chain E: R.193 Ligands: CD.45, ACT.49, ACT.50 4 PLIP interactions: 4 interactions with chain E Water bridges: E:R.193, E:R.193, E:R.193 Salt bridges: E:R.193 ACT.49: 3 residues within 4Å: Ligands: ACT.41, CD.45, ACT.50 No protein-ligand interaction detected (PLIP) ACT.50: 3 residues within 4Å: Ligands: ACT.41, CD.45, ACT.49 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:K.130

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

GHE.5: 10 residues within 4Å: Chain A: D.58, N.59, L.62, Y.64, Y.74, E.136, D.138, Q.148 Ligands: CD.7, CD.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.62, A:Y.64 Hydrogen bonds: A:N.59, A:Q.148 GHE.17: 10 residues within 4Å: Chain B: D.58, N.59, L.62, Y.64, Y.74, E.136, D.138, Q.148 Ligands: CD.19, CD.20 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.62, B:Y.64 Hydrogen bonds: B:N.59, B:Q.148 Water bridges: B:Y.74 GHE.29: 10 residues within 4Å: Chain C: D.58, N.59, L.62, Y.64, Y.74, E.136, D.138, Q.148 Ligands: CD.27, CD.28 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:D.58 GHE.35: 10 residues within 4Å: Chain D: D.58, N.59, L.62, Y.64, Y.74, E.136, D.138, Q.148 Ligands: CD.36, CD.37 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.62, D:Y.64 Hydrogen bonds: D:N.59, D:N.59, D:Q.148 GHE.42: 10 residues within 4Å: Chain E: D.58, N.59, L.62, Y.64, Y.74, E.136, D.138, Q.148 Ligands: CD.43, CD.44 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:L.62, E:Y.64 Hydrogen bonds: E:N.59, E:N.59, E:Q.148

35 x CD: CADMIUM ION(Non-covalent)(Non-functional Binders)

CD.7: 5 residues within 4Å: Chain A: E.136, D.138, Q.148 Ligands: GHE.5, CD.8 Ligand excluded by PLIP CD.8: 7 residues within 4Å: Chain A: D.58, N.59, E.136, Q.137, D.138 Ligands: GHE.5, CD.7 Ligand excluded by PLIP CD.9: 2 residues within 4Å: Chain A: E.14 Ligands: CD.15 Ligand excluded by PLIP CD.10: 4 residues within 4Å: Ligands: ACT.3, ACT.4, ACT.6, ACT.13 Ligand excluded by PLIP CD.11: 2 residues within 4Å: Chain A: D.145, S.147 Ligand excluded by PLIP CD.14: 1 residues within 4Å: Chain A: K.143 Ligand excluded by PLIP CD.15: 1 residues within 4Å: Ligands: CD.9 Ligand excluded by PLIP CD.16: 1 residues within 4Å: Chain A: Q.55 Ligand excluded by PLIP CD.19: 7 residues within 4Å: Chain B: D.58, N.59, E.136, Q.137, D.138 Ligands: GHE.17, CD.20 Ligand excluded by PLIP CD.20: 5 residues within 4Å: Chain B: E.136, D.138, Q.148 Ligands: GHE.17, CD.19 Ligand excluded by PLIP CD.21: 2 residues within 4Å: Chain B: E.14 Ligands: CD.24 Ligand excluded by PLIP CD.22: 1 residues within 4Å: Ligands: ACT.18 Ligand excluded by PLIP CD.24: 1 residues within 4Å: Ligands: CD.21 Ligand excluded by PLIP CD.25: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CD.26: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CD.27: 7 residues within 4Å: Chain C: D.58, N.59, E.136, Q.137, D.138 Ligands: CD.28, GHE.29 Ligand excluded by PLIP CD.28: 5 residues within 4Å: Chain C: E.136, D.138, Q.148 Ligands: CD.27, GHE.29 Ligand excluded by PLIP CD.30: 2 residues within 4Å: Chain C: D.145, S.147 Ligand excluded by PLIP CD.32: 2 residues within 4Å: Chain C: E.14 Ligands: CD.33 Ligand excluded by PLIP CD.33: 1 residues within 4Å: Ligands: CD.32 Ligand excluded by PLIP CD.34: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CD.36: 5 residues within 4Å: Chain D: E.136, D.138, Q.148 Ligands: GHE.35, CD.37 Ligand excluded by PLIP CD.37: 7 residues within 4Å: Chain D: D.58, N.59, E.136, Q.137, D.138 Ligands: GHE.35, CD.36 Ligand excluded by PLIP CD.38: 2 residues within 4Å: Chain D: D.145, S.147 Ligand excluded by PLIP CD.39: 2 residues within 4Å: Chain D: E.14 Ligands: CD.40 Ligand excluded by PLIP CD.40: 1 residues within 4Å: Ligands: CD.39 Ligand excluded by PLIP CD.43: 7 residues within 4Å: Chain E: D.58, N.59, E.136, Q.137, D.138 Ligands: GHE.42, CD.44 Ligand excluded by PLIP CD.44: 5 residues within 4Å: Chain E: E.136, D.138, Q.148 Ligands: GHE.42, CD.43 Ligand excluded by PLIP CD.45: 4 residues within 4Å: Ligands: ACT.41, ACT.49, ACT.50, CD.53 Ligand excluded by PLIP CD.46: 2 residues within 4Å: Chain E: D.145, S.147 Ligand excluded by PLIP CD.47: 2 residues within 4Å: Chain E: E.14 Ligands: CD.51 Ligand excluded by PLIP CD.51: 1 residues within 4Å: Ligands: CD.47 Ligand excluded by PLIP CD.52: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CD.53: 2 residues within 4Å: Ligands: CD.45, CD.54 Ligand excluded by PLIP CD.54: 1 residues within 4Å: Ligands: CD.53 Ligand excluded by PLIP

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

NAG.12: 3 residues within 4Å: Chain A: Q.31, N.32, S.101 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.31, A:N.32, A:E.99 Water bridges: A:E.99, A:E.99 NAG.31: 4 residues within 4Å: Chain C: Q.31, N.32, E.99, S.101 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.32, C:S.101 NAG.48: 3 residues within 4Å: Chain E: Q.31, N.32, S.101 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Q.31, E:N.32

1 x SIA: N-acetyl-alpha-neuraminic acid(Non-covalent)

SIA.23: 5 residues within 4Å: Chain B: T.2, Y.190, E.191, I.192, R.193 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.190, B:Y.190, B:I.192, B:R.193, B:R.193 Water bridges: B:T.2, B:Y.190

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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