SMTL ID : 3kqr.1

The structure of serum amyloid p component bound to phosphoethanolamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-pentamer

Ligands

5 x OPE: PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER(Non-covalent)

OPE.1: 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.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.59, A:Y.74, A:Q.148 Water bridges: A:K.79 OPE.5: 11 residues within 4Å: Chain B: D.58, N.59, L.62, Y.64, Y.74, K.79, E.136, D.138, Q.148 Ligands: CA.6, CA.8 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.59, B:Y.74, B:Q.148 Water bridges: B:Y.74, B:K.79 OPE.9: 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 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.59, C:Y.74, C:Q.148 Water bridges: C:R.77, C:K.79 OPE.13: 11 residues within 4Å: Chain D: D.58, N.59, L.62, Y.64, Y.74, K.79, E.136, D.138, Q.148 Ligands: CA.14, CA.16 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.58, D:N.59, D:Y.74, D:Q.148 Water bridges: D:K.79 OPE.17: 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.20 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:N.59, E:Y.74, E:Q.148 Water bridges: E:K.79

10 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: E.136, D.138, D.145, Q.148 Ligands: OPE.1, CA.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.136, A:D.138, A:D.138, H2O.1, H2O.1 CA.4: 8 residues within 4Å: Chain A: N.53, D.58, N.59, E.136, Q.137, D.138 Ligands: OPE.1, CA.2 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.6: 8 residues within 4Å: Chain B: N.53, D.58, N.59, E.136, Q.137, D.138 Ligands: OPE.5, CA.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.8: 6 residues within 4Å: Chain B: E.136, D.138, D.145, Q.148 Ligands: OPE.5, CA.6 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.136, B:D.138, B:D.138, H2O.11, H2O.11 CA.10: 6 residues within 4Å: Chain C: E.136, D.138, D.145, Q.148 Ligands: OPE.9, CA.11 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.136, C:D.138, C:D.138, H2O.22, H2O.23 CA.11: 8 residues within 4Å: Chain C: N.53, D.58, N.59, E.136, Q.137, D.138 Ligands: OPE.9, CA.10 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.14: 6 residues within 4Å: Chain D: E.136, D.138, D.145, Q.148 Ligands: OPE.13, CA.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.34, H2O.34 CA.16: 8 residues within 4Å: Chain D: N.53, D.58, N.59, E.136, Q.137, D.138 Ligands: OPE.13, CA.14 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: 6 residues within 4Å: Chain E: E.136, D.138, D.145, Q.148 Ligands: OPE.17, CA.20 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.136, E:D.138, E:D.138, H2O.45, H2O.45 CA.20: 8 residues within 4Å: Chain E: N.53, D.58, N.59, E.136, Q.137, D.138 Ligands: OPE.17, CA.18 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

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

NAG.3: 5 residues within 4Å: Chain A: Q.31, N.32, E.99, S.101, V.163 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.31 Hydrogen bonds: A:N.32, A:E.99 Water bridges: A:Q.31 NAG.7: 5 residues within 4Å: Chain B: Q.31, N.32, E.99, S.101, V.163 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.99 Water bridges: B:Q.31, B:V.163 NAG.12: 5 residues within 4Å: Chain C: Q.31, N.32, E.99, S.101, D.161 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.31 Water bridges: C:Q.31, C:N.32, C:N.32 NAG.15: 5 residues within 4Å: Chain D: K.28, Q.31, N.32, E.99, S.101 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.31, D:N.32 NAG.19: 4 residues within 4Å: Chain E: Q.31, N.32, S.101, F.124 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Q.31, E:N.32 Water bridges: E:Q.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mikolajek, H. et al., Structural basis of ligand specificity in the human pentraxins, C-reactive protein and serum amyloid P component. J.Mol.Recognit. (2011)

Release Date

2010-12-08

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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