SMTL ID : 9nb6.1

Cryo-EM structure of the CD163/Hp(1-1)Hb complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.30 Å

Oligo State

hetero-3-1-1-2-mer

Ligands

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

NAG.1: 7 residues within 4Å: Chain A: D.229, G.230, V.231, N.279, A.280, S.281, R.351 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.229, A:R.351 NAG.2: 1 residues within 4Å: Chain A: N.404 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.404 NAG.3: 1 residues within 4Å: Chain A: N.726 No protein-ligand interaction detected (PLIP) NAG.13: 2 residues within 4Å: Chain B: D.229, N.279 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.229 NAG.14: 2 residues within 4Å: Chain B: N.402, N.404 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.404 NAG.15: 2 residues within 4Å: Chain B: N.726, H.732 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.726 NAG.24: 5 residues within 4Å: Chain C: D.229, G.230, V.231, N.279, R.351 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.229, C:D.229, C:N.279, C:R.351, C:R.351 NAG.25: 1 residues within 4Å: Chain C: N.404 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:N.404 NAG.26: 1 residues within 4Å: Chain C: N.726 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.726

23 x CA: CALCIUM ION(Non-covalent)

CA.4: 2 residues within 4Å: Chain A: D.145, E.211 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.145, A:E.211 CA.5: 4 residues within 4Å: Chain A: D.145, D.183, D.184, N.206 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.145, A:D.183, A:D.184 CA.6: 3 residues within 4Å: Chain A: D.251, D.252, E.318 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.251, A:D.252, A:E.318 CA.7: 6 residues within 4Å: Chain A: G.253, D.255, D.258, V.292, S.293, C.294 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:G.253, A:D.255, A:D.258, A:V.292 CA.8: 4 residues within 4Å: Chain A: D.704, D.705, E.771 Chain C: E.940 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.705, A:E.771 CA.9: 5 residues within 4Å: Chain A: S.706, D.711, M.745, K.746, C.747 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:S.706, A:D.711, A:M.745 CA.10: 4 residues within 4Å: Chain A: D.743, E.744, N.766, C.767 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.743, A:D.743, A:E.744, A:E.744 CA.11: 3 residues within 4Å: Chain A: D.914, D.915, E.981 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.981 CA.12: 6 residues within 4Å: Chain A: S.916, D.918, D.921, V.955, K.956, C.957 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:S.916, A:D.918, A:D.921, A:D.921, A:V.955 CA.16: 4 residues within 4Å: Chain B: D.251, D.252, E.318 Chain E: K.83 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.252, B:E.318 CA.17: 6 residues within 4Å: Chain B: G.253, D.255, D.258, V.292, S.293, C.294 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:G.253, B:D.255, B:V.292 CA.18: 4 residues within 4Å: Chain A: E.940 Chain B: D.704, D.705, E.771 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.704, B:D.705, B:E.771 CA.19: 6 residues within 4Å: Chain B: S.706, D.708, D.711, M.745, K.746, C.747 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.708, B:D.711, B:D.711, B:M.745 CA.20: 5 residues within 4Å: Chain B: D.705, D.743, E.744, N.766, C.767 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.705, B:D.743, B:D.743, B:E.744 CA.21: 4 residues within 4Å: Chain B: D.914, D.915, E.981 Chain C: K.770 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.915, B:E.981, B:E.981 CA.22: 5 residues within 4Å: Chain B: S.916, D.918, D.921, V.955, K.956 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:S.916, B:D.918, B:D.921, B:D.921, B:V.955 CA.23: 3 residues within 4Å: Chain B: E.940 Chain C: D.705, E.771 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Metal complexes: C:D.705, C:E.771, B:E.940 CA.27: 3 residues within 4Å: Chain C: D.251, D.252, E.318 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.251, C:D.252, C:E.318 CA.28: 5 residues within 4Å: Chain C: G.253, D.255, V.292, S.293, C.294 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:G.253, C:D.255, C:V.292 CA.29: 6 residues within 4Å: Chain C: S.706, D.708, D.711, M.745, K.746, C.747 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.708, C:D.711, C:D.711, C:M.745 CA.30: 4 residues within 4Å: Chain C: D.705, D.743, E.744, N.766 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.705, C:E.744 CA.31: 3 residues within 4Å: Chain C: D.914, D.915, E.981 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.914 CA.32: 4 residues within 4Å: Chain C: S.916, D.918, D.921, V.955 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:S.916, C:D.918, C:D.921, C:V.955

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.33: 18 residues within 4Å: Chain D: T.40, Y.43, F.44, F.47, H.59, K.62, V.63, L.67, L.84, H.88, L.92, V.94, N.98, F.99, L.102, V.133, L.137 Ligands: OXY.34 18 PLIP interactions: 18 interactions with chain D, Hydrophobic interactions: D:T.40, D:Y.43, D:F.44, D:F.44, D:F.47, D:K.62, D:V.63, D:L.67, D:L.84, D:L.92, D:V.94, D:V.94, D:N.98, D:F.99, D:V.133, D:L.137 Salt bridges: D:K.62 Metal complexes: D:H.88 HEM.35: 15 residues within 4Å: Chain E: F.42, F.43, H.64, K.67, V.68, A.71, L.89, H.93, K.96, L.97, N.103, F.104, L.107, L.142 Ligands: OXY.36 16 PLIP interactions: 16 interactions with chain E, Hydrophobic interactions: E:F.42, E:F.42, E:F.43, E:F.43, E:K.67, E:A.71, E:L.89, E:L.97, E:N.103, E:F.104, E:F.104, E:L.142 Salt bridges: E:K.67, E:K.96 pi-Stacking: E:H.64 Metal complexes: E:H.93

2 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.34: 6 residues within 4Å: Chain D: L.30, F.44, H.59, V.63, L.102 Ligands: HEM.33 No protein-ligand interaction detected (PLIP) OXY.36: 6 residues within 4Å: Chain E: L.29, F.43, H.64, V.68, L.107 Ligands: HEM.35 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
Hemoglobin subunit alpha: D
Hemoglobin subunit beta: E
Isoform 2 of Haptoglobin: FG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

Scavenger receptor cysteine-rich type 1 protein M130

Hemoglobin subunit alpha

Hemoglobin subunit beta

Isoform 2 of Haptoglobin

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