SMTL ID : 9u4e.1

Cryo-EM structure of the human CRP-CPS23F complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.78 Å

Oligo State

homo-pentamer

Ligands

5 x BGC- RM4- 01- RAM: alpha-L-rhamnopyranose-(1-2)-1,3-bis(oxidanyl)propan-2-yl [(2~{R},3~{S},4~{S},5~{R})-2-(hydroxymethyl)-3,5,6-tris(oxidanyl)oxan-4-yl] hydrogen phosphate-(1-4)-beta-L-rhamnopyranose-(1-4)-beta-D-glucopyranose

BGC-RM4-01-RAM.1: 13 residues within 4Å: Chain A: Q.77, D.78, N.79, L.82, F.84, T.94, E.156, D.158, N.163, E.165, Q.168 Ligands: CA.6, CA.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.79, A:Q.168 BGC-RM4-01-RAM.2: 14 residues within 4Å: Chain B: Q.77, D.78, N.79, L.82, F.84, S.92, T.94, E.99, E.156, D.158, E.165, Q.168 Ligands: CA.8, CA.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.79, B:E.99, B:Q.168, B:D.78, B:D.158 BGC-RM4-01-RAM.3: 14 residues within 4Å: Chain C: Q.77, D.78, N.79, L.82, F.84, S.92, E.99, E.156, Q.157, D.158, E.165, Q.168 Ligands: CA.10, CA.11 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.79, C:N.79, C:Q.168, C:Q.77, C:D.78 BGC-RM4-01-RAM.4: 11 residues within 4Å: Chain D: D.78, N.79, L.82, F.84, E.99, E.156, D.158, E.165, Q.168 Ligands: CA.12, CA.13 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.79, D:E.99, D:E.156, D:Q.168, D:N.79 BGC-RM4-01-RAM.5: 11 residues within 4Å: Chain E: D.78, N.79, L.82, F.84, E.156, D.158, N.163, E.165, Q.168 Ligands: CA.14, CA.15 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.79, E:Q.168

10 x CA: CALCIUM ION(Non-covalent)

CA.6: 5 residues within 4Å: Chain A: E.156, D.158, E.165, Q.168 Ligands: BGC-RM4-01-RAM.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.158, A:D.158, A:E.165, A:E.165 CA.7: 6 residues within 4Å: Chain A: D.78, N.79, E.156, Q.157, D.158 Ligands: BGC-RM4-01-RAM.1 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.78, A:E.156, A:E.156, A:Q.157, A:D.158 CA.8: 6 residues within 4Å: Chain B: E.156, D.158, E.165, Q.168 Ligands: BGC-RM4-01-RAM.2, CA.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.156, B:D.158, B:D.158, B:E.165 CA.9: 7 residues within 4Å: Chain B: D.78, N.79, E.156, Q.157, D.158 Ligands: BGC-RM4-01-RAM.2, CA.8 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.78, B:E.156, B:E.156, B:Q.157, B:D.158 CA.10: 5 residues within 4Å: Chain C: E.156, D.158, E.165, Q.168 Ligands: BGC-RM4-01-RAM.3 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.156, C:D.158, C:D.158, C:E.165 CA.11: 7 residues within 4Å: Chain C: D.78, N.79, E.156, Q.157, D.158 Ligands: BGC-RM4-01-RAM.3, BGC-RM4-01-RAM.3 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.78, C:E.156, C:E.156, C:Q.157, C:D.158 CA.12: 5 residues within 4Å: Chain D: E.156, D.158, E.165, Q.168 Ligands: BGC-RM4-01-RAM.4 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.158, D:D.158, D:E.165, D:E.165 CA.13: 7 residues within 4Å: Chain D: D.78, N.79, E.156, Q.157, D.158 Ligands: BGC-RM4-01-RAM.4, BGC-RM4-01-RAM.4 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.78, D:E.156, D:E.156, D:Q.157, D:D.158 CA.14: 5 residues within 4Å: Chain E: E.156, D.158, E.165, Q.168 Ligands: BGC-RM4-01-RAM.5 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:E.156, E:D.158, E:D.158, E:E.165 CA.15: 6 residues within 4Å: Chain E: D.78, N.79, E.156, Q.157, D.158 Ligands: BGC-RM4-01-RAM.5 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.78, E:E.156, E:E.156, E:Q.157, E:D.158

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, D.Y. et al., Cryo-EM structure of the human CRP-CPS23F complex. To Be Published

Release Date

2025-09-24

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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