SMTL ID : 7pke.1

C-reactive protein pentamer at pH 7.5 with phosphocholine ligand

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

10 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: E.138, D.140, E.147, Q.150 Ligands: PC.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.138, A:D.140, A:D.140 CA.2: 6 residues within 4Å: Chain A: D.60, N.61, E.138, Q.139, D.140 Ligands: PC.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.60, A:E.138 CA.4: 5 residues within 4Å: Chain B: E.138, D.140, E.147, Q.150 Ligands: PC.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.140, B:D.140 CA.5: 6 residues within 4Å: Chain B: D.60, N.61, E.138, Q.139, D.140 Ligands: PC.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.60, B:E.138, B:Q.139, B:D.140 CA.7: 6 residues within 4Å: Chain C: E.138, D.140, E.147, Q.150 Ligands: CA.8, PC.9 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.138, C:D.140, C:D.140, C:E.147 CA.8: 7 residues within 4Å: Chain C: D.60, N.61, E.138, Q.139, D.140 Ligands: CA.7, PC.9 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.60, C:E.138, C:E.138, C:D.140 CA.10: 6 residues within 4Å: Chain D: E.138, D.140, E.147, Q.150 Ligands: CA.11, PC.12 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.138, D:D.140, D:D.140 CA.11: 7 residues within 4Å: Chain D: D.60, N.61, E.138, Q.139, D.140 Ligands: CA.10, PC.12 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.60, D:E.138, D:E.138, D:Q.139, D:D.140 CA.13: 6 residues within 4Å: Chain E: E.138, D.140, E.147, Q.150 Ligands: CA.14, PC.15 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:E.138, E:D.140, E:D.140, E:E.147 CA.14: 7 residues within 4Å: Chain E: D.60, N.61, E.138, Q.139, D.140 Ligands: CA.13, PC.15 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.60, E:E.138, E:E.138, E:Q.139, E:D.140

5 x PC: PHOSPHOCHOLINE(Non-covalent)

PC.3: 12 residues within 4Å: Chain A: D.60, N.61, L.64, F.66, S.74, T.76, E.81, E.138, D.140, Q.150 Ligands: CA.1, CA.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.61, A:Q.150 Salt bridges: A:E.81 pi-Cation interactions: A:F.66 PC.6: 12 residues within 4Å: Chain B: D.60, N.61, L.64, F.66, S.74, T.76, E.81, E.138, D.140, Q.150 Ligands: CA.4, CA.5 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.61, B:Q.150 Salt bridges: B:E.81, B:E.138 pi-Cation interactions: B:F.66 PC.9: 13 residues within 4Å: Chain C: D.60, N.61, L.64, F.66, S.68, S.74, E.81, E.138, D.140, E.147, Q.150 Ligands: CA.7, CA.8 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.61, C:Q.150 Salt bridges: C:E.81 pi-Cation interactions: C:F.66 PC.12: 12 residues within 4Å: Chain D: D.60, N.61, L.64, F.66, S.74, T.76, E.81, E.138, D.140, Q.150 Ligands: CA.10, CA.11 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:N.61, D:E.138, D:E.147, D:Q.150 Salt bridges: D:E.81 pi-Cation interactions: D:F.66 PC.15: 14 residues within 4Å: Chain E: D.60, N.61, L.64, F.66, S.68, S.74, T.76, E.81, E.138, D.140, E.147, Q.150 Ligands: CA.13, CA.14 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:N.61, E:E.138, E:Q.150 Salt bridges: E:E.81 pi-Cation interactions: E:F.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Noone, D.P. et al., Cryo-Electron Microscopy and Biochemical Analysis Offer Insights Into the Effects of Acidic pH, Such as Occur During Acidosis, on the Complement Binding Properties of C-Reactive Protein. Front Immunol (2021)

Release Date

2021-12-22

Peptides

C-reactive protein: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
D

C
C

D
B

E
A

C-reactive protein

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