SMTL ID : 9nb5.1

Cryo-EM structure of the autoinhibitory CD163 trimer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.00 Å

Oligo State

homo-trimer

Ligands

20 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: G.253, D.255, D.258, V.292, S.293 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:G.253, A:D.255, A:D.258, A:D.258, A:V.292 CA.2: 4 residues within 4Å: Chain A: H.570, D.572, D.575, F.609 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.570, A:D.575, A:F.609 CA.3: 3 residues within 4Å: Chain A: D.704, D.705, E.771 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.704, A:D.705, A:E.771 CA.4: 5 residues within 4Å: Chain A: S.706, D.711, M.745, K.746, C.747 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:S.706, A:D.711, A:D.711, A:M.745 CA.5: 4 residues within 4Å: Chain A: D.705, D.743, E.744, N.766 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.744 CA.6: 3 residues within 4Å: Chain A: D.914, D.915, E.981 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.914, A:D.915, A:E.981 CA.7: 5 residues within 4Å: Chain A: S.916, D.918, D.921, V.955, K.956 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:S.916, A:D.918, A:D.921, A:V.955 CA.11: 4 residues within 4Å: Chain A: K.311 Chain B: D.251, D.252, E.318 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.252, B:E.318 CA.12: 5 residues within 4Å: Chain B: G.253, D.255, D.258, V.292, S.293 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:G.253, B:D.255, B:D.258, B:D.258, B:V.292 CA.13: 4 residues within 4Å: Chain B: H.570, D.572, D.575, F.609 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.575, B:D.575, B:F.609 CA.14: 4 residues within 4Å: Chain A: E.940 Chain B: D.704, D.705, E.771 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.705, B:E.771 CA.15: 4 residues within 4Å: Chain B: S.706, D.708, D.711, M.745 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.708, B:D.711, B:D.711 CA.16: 4 residues within 4Å: Chain B: D.705, D.743, E.744, N.766 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.743, B:E.744 CA.17: 5 residues within 4Å: Chain B: S.916, D.918, D.921, V.955, K.956 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:S.916, B:D.918, B:D.921, B:V.955 CA.21: 3 residues within 4Å: Chain C: D.251, D.252, E.318 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.252 CA.22: 5 residues within 4Å: Chain C: G.253, D.255, D.258, V.292, S.293 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:G.253, C:D.255, C:D.258, C:V.292 CA.23: 4 residues within 4Å: Chain C: H.570, D.572, D.575, F.609 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.570, C:D.575, C:D.575, C:F.609 CA.24: 4 residues within 4Å: Chain C: S.706, D.711, M.745, K.746 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:S.706, C:D.711, C:D.711, C:M.745 CA.25: 3 residues within 4Å: Chain C: D.914, D.915, E.981 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.915, C:E.981 CA.26: 6 residues within 4Å: Chain C: S.916, D.918, D.921, V.955, K.956, C.957 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:S.916, C:D.918, C:D.921, C:V.955

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

NAG.8: 4 residues within 4Å: Chain A: D.229, G.230, V.231, N.279 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.229, A:D.229, A:N.279 NAG.9: 1 residues within 4Å: Chain A: N.404 No protein-ligand interaction detected (PLIP) NAG.10: 3 residues within 4Å: Chain A: N.726, T.728, H.732 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.726 NAG.18: 2 residues within 4Å: Chain B: N.279, S.281 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.279 NAG.19: 1 residues within 4Å: Chain B: N.404 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.404 NAG.20: 3 residues within 4Å: Chain B: N.726, H.732, I.776 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.776 Hydrogen bonds: B:N.726 NAG.27: 5 residues within 4Å: Chain C: D.229, V.231, N.279, A.280, S.281 No protein-ligand interaction detected (PLIP) NAG.28: 1 residues within 4Å: Chain C: N.404 No protein-ligand interaction detected (PLIP) NAG.29: 1 residues within 4Å: Chain C: N.726 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, C.-S. et al., Structural elucidation of the haptoglobin-hemoglobin clearance mechanism by macrophage scavenger receptor CD163. To Be Published

Release Date

2025-06-18

Peptides

Scavenger receptor cysteine-rich type 1 protein M130: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Scavenger receptor cysteine-rich type 1 protein M130

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