SMTL ID : 9nb8.1

Cryo-EM structure of the CD163/HpSPHb complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 4.00 Å

Oligo State

hetero-3-1-1-1-mer

Ligands

21 x CA: CALCIUM ION(Non-covalent)

CA.1: 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.2: 3 residues within 4Å: Chain A: D.144, D.145, E.211 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.144, A:D.145, A:E.211 CA.3: 2 residues within 4Å: Chain A: D.252, E.318 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.252, A:D.252, A:E.318, A:E.318 CA.4: 5 residues within 4Å: Chain A: G.253, D.255, D.258, V.292, S.293 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.255, A:D.258, A:V.292 CA.5: 4 residues within 4Å: Chain A: D.704, D.705, E.771 Chain C: E.940 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Metal complexes: A:D.705, A:E.771, C:E.940, C:E.940 CA.6: 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.7: 5 residues within 4Å: Chain A: D.743, E.744, N.766, C.767 Chain C: K.980 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.744 CA.8: 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.9: 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.10: 3 residues within 4Å: Chain B: D.251, D.252, E.318 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.251, B:D.252, B:E.318 CA.11: 6 residues within 4Å: Chain B: G.253, D.255, D.258, V.292, S.293, C.294 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:G.253, B:D.255, B:D.258, B:V.292 CA.12: 5 residues within 4Å: Chain A: E.940, K.980 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.13: 5 residues within 4Å: Chain B: S.706, D.711, M.745, K.746, C.747 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:S.706, B:D.711, B:D.711, B:M.745 CA.14: 5 residues within 4Å: Chain A: K.980 Chain B: D.705, D.743, E.744, N.766 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.744 CA.15: 5 residues within 4Å: Chain B: D.914, D.915, E.981 Chain C: K.770, E.771 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.915, B:E.981, B:E.981 CA.16: 4 residues within 4Å: Chain B: S.916, D.918, D.921, V.955 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:S.916, B:D.918, B:D.921, B:V.955 CA.17: 4 residues within 4Å: Chain B: K.980 Chain C: D.704, D.705, E.771 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.771 CA.18: 5 residues within 4Å: Chain C: S.706, D.708, D.711, M.745, K.746 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:S.706, C:D.708, C:D.711, C:M.745 CA.19: 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.20: 1 residues within 4Å: Chain C: D.914 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.914 CA.21: 5 residues within 4Å: Chain C: S.916, D.918, D.921, V.955, K.956 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(Covalent)(Non-covalent)

HEM.22: 15 residues within 4Å: Chain D: M.33, F.44, H.59, K.62, A.66, L.84, L.87, H.88, L.92, N.98, F.99, L.102, V.133, L.137 Ligands: OXY.23 11 PLIP interactions: 11 interactions with chain D, Hydrophobic interactions: D:K.62, D:A.66, D:L.84, D:L.92, D:F.99, D:V.133, D:L.137 Salt bridges: D:K.62, D:K.62 pi-Stacking: D:H.59 Metal complexes: D:H.88 HEM.24: 16 residues within 4Å: Chain E: T.39, F.42, F.43, F.46, H.64, K.67, V.68, A.71, L.92, H.93, L.97, V.99, N.103, F.104, L.142 Ligands: OXY.25 19 PLIP interactions: 19 interactions with chain E, Hydrophobic interactions: E:T.39, E:F.42, E:F.43, E:F.46, E:K.67, E:K.67, E:A.71, E:L.92, E:L.97, E:V.99, E:V.99, E:N.103, E:F.104, E:F.104, E:L.142 Salt bridges: E:H.64, E:K.67, E:K.96 pi-Stacking: E:H.93

2 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.23: 4 residues within 4Å: Chain D: L.30, H.59, V.63 Ligands: HEM.22 No protein-ligand interaction detected (PLIP) OXY.25: 3 residues within 4Å: Chain E: H.64, V.68 Ligands: HEM.24 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
Haptoglobin: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Scavenger receptor cysteine-rich type 1 protein M130

Hemoglobin subunit alpha

Hemoglobin subunit beta

Haptoglobin

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