SMTL ID : 7pkh.1

C-reactive protein decamer at pH 5 with phosphocholine ligand

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-10-mer

Ligands

20 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: E.138, D.140, E.147, Q.150 Ligands: CA.2, PC.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.138, A:D.140, A:D.140, A:E.147 CA.2: 7 residues within 4Å: Chain A: D.60, N.61, E.138, Q.139, D.140 Ligands: CA.1, PC.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.60, A:E.138, A:E.138, A:Q.139, A:D.140 CA.4: 5 residues within 4Å: Chain B: E.138, D.140, E.147, Q.150 Ligands: PC.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.138, 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: 5 residues within 4Å: Chain C: E.138, D.140, E.147, Q.150 Ligands: 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: 6 residues within 4Å: Chain C: D.60, N.61, E.138, Q.139, D.140 Ligands: PC.9 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.60, C:E.138, C:Q.139, 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 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.60, 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 3 PLIP interactions: 3 interactions with chain E Metal complexes: 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 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.60, E:E.138, E:Q.139, E:D.140 CA.16: 6 residues within 4Å: Chain F: E.138, D.140, E.147, Q.150 Ligands: CA.17, PC.18 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.140, F:D.140, F:E.147 CA.17: 7 residues within 4Å: Chain F: D.60, N.61, E.138, Q.139, D.140 Ligands: CA.16, PC.18 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.60, F:Q.139, F:D.140 CA.19: 6 residues within 4Å: Chain G: E.138, D.140, E.147, Q.150 Ligands: CA.20, PC.21 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.138, G:D.140, G:D.140 CA.20: 7 residues within 4Å: Chain G: D.60, N.61, E.138, Q.139, D.140 Ligands: CA.19, PC.21 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:D.60, G:E.138, G:E.138, G:Q.139, G:D.140 CA.22: 6 residues within 4Å: Chain H: E.138, D.140, E.147, Q.150 Ligands: CA.23, PC.24 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:E.138, H:D.140, H:D.140, H:E.147 CA.23: 7 residues within 4Å: Chain H: D.60, N.61, E.138, Q.139, D.140 Ligands: CA.22, PC.24 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:D.60, H:E.138, H:E.138, H:Q.139, H:D.140 CA.25: 6 residues within 4Å: Chain I: E.138, D.140, E.147, Q.150 Ligands: CA.26, PC.27 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:E.138, I:D.140, I:D.140, I:E.147 CA.26: 7 residues within 4Å: Chain I: D.60, N.61, E.138, Q.139, D.140 Ligands: CA.25, PC.27 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:D.60, I:E.138, I:E.138, I:Q.139, I:D.140 CA.28: 5 residues within 4Å: Chain J: E.138, D.140, E.147, Q.150 Ligands: PC.30 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:E.138, J:D.140, J:D.140 CA.29: 6 residues within 4Å: Chain J: D.60, N.61, E.138, Q.139, D.140 Ligands: PC.30 5 PLIP interactions: 5 interactions with chain J Metal complexes: J:D.60, J:E.138, J:E.138, J:Q.139, J:D.140

10 x PC: PHOSPHOCHOLINE(Non-covalent)

PC.3: 14 residues within 4Å: Chain A: 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.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: 14 residues within 4Å: Chain B: 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.4, CA.5 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.61, B:D.140, B:Q.150 Salt bridges: B:E.81 pi-Cation interactions: B:F.66 PC.9: 12 residues within 4Å: Chain C: D.60, N.61, L.64, F.66, S.74, T.76, E.81, E.138, D.140, Q.150 Ligands: CA.7, CA.8 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.61, C:E.138, C:Q.150, C:Q.150 pi-Cation interactions: C:F.66 PC.12: 13 residues within 4Å: Chain D: D.60, N.61, L.64, F.66, S.68, 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:Q.150, 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 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:N.61, E:D.140, E:Q.150 pi-Cation interactions: E:F.66 PC.18: 14 residues within 4Å: Chain F: 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.16, CA.17 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:N.61, F:Q.150 Salt bridges: F:E.81 pi-Cation interactions: F:F.66 PC.21: 13 residues within 4Å: Chain G: D.60, N.61, L.64, F.66, S.68, S.74, T.76, E.81, E.138, D.140, Q.150 Ligands: CA.19, CA.20 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:D.140, G:D.140, G:Q.150 Salt bridges: G:E.81 pi-Cation interactions: G:F.66 PC.24: 14 residues within 4Å: Chain H: 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.22, CA.23 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:N.61, H:Q.150 Salt bridges: H:E.81 pi-Cation interactions: H:F.66 PC.27: 14 residues within 4Å: Chain I: 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.25, CA.26 4 PLIP interactions: 4 interactions with chain I Hydrogen bonds: I:N.61, I:Q.150 Salt bridges: I:E.81 pi-Cation interactions: I:F.66 PC.30: 13 residues within 4Å: Chain J: D.60, N.61, L.64, F.66, S.68, S.74, T.76, E.81, E.138, D.140, Q.150 Ligands: CA.28, CA.29 3 PLIP interactions: 3 interactions with chain J Hydrogen bonds: J:Q.150 Salt bridges: J:E.81 pi-Cation interactions: J: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: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
J

B
F

C
G

D
H

E
I

F
E

G
D

H
C

I
B

J
A

C-reactive protein

Related Entries With Identical Sequence