SMTL ID : 7tba.1 (3 other biounits)

Pentraxin - ligand complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

homo-pentamer

Ligands

5 x XQY: [3-(dibutylamino)propyl]phosphonic acid(Non-covalent)

XQY.1: 14 residues within 4Å: Chain A: N.61, L.64, F.66, S.68, S.74, T.76, G.79, E.81, E.138, D.140, E.147, Q.150 Ligands: CA.2, CA.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.66 Hydrogen bonds: A:E.138, A:E.138, A:E.138, A:Q.150 Salt bridges: A:E.81 XQY.4: 14 residues within 4Å: Chain B: N.61, L.64, F.66, S.68, S.74, T.76, G.79, E.81, E.138, D.140, E.147, Q.150 Ligands: CA.5, CA.6 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.66 Hydrogen bonds: B:Q.150, B:Q.150 Salt bridges: B:E.81 XQY.7: 14 residues within 4Å: Chain C: N.61, L.64, F.66, S.68, S.74, T.76, G.79, E.81, E.138, D.140, E.147, Q.150 Ligands: CA.8, CA.9 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.66 Hydrogen bonds: C:E.147, C:Q.150 Salt bridges: C:E.81 XQY.10: 14 residues within 4Å: Chain D: N.61, L.64, F.66, S.68, S.74, T.76, G.79, E.81, E.138, D.140, E.147, Q.150 Ligands: CA.11, CA.12 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:F.66 Hydrogen bonds: D:E.147, D:Q.150 Salt bridges: D:E.81 XQY.13: 14 residues within 4Å: Chain E: N.61, L.64, F.66, S.68, S.74, T.76, G.79, E.81, E.138, D.140, E.147, Q.150 Ligands: CA.14, CA.15 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:F.66 Hydrogen bonds: E:Q.150, E:Q.150 Salt bridges: E:E.81

10 x CA: CALCIUM ION(Non-covalent)

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zeller, J. et al., A novel phosphocholine-mimetic inhibits a pro-inflammatory conformational change in C-reactive protein. Embo Mol Med (2023)

Release Date

2022-10-19

Peptides

C-reactive protein: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

C-reactive protein

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