SMTL ID : 9hej.1

Dimeric CD163 bound to human haptoglobin-haemoglobin complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-2-mer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: V.272, N.320, L.393 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.272 NAG-NAG.2: 2 residues within 4Å: Chain B: I.766, N.767 No protein-ligand interaction detected (PLIP)

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

NAG.3: 2 residues within 4Å: Chain A: N.443, N.445 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.443 NAG.4: 3 residues within 4Å: Chain A: L.976, F.979, N.1027 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1027 NAG.11: 4 residues within 4Å: Chain B: D.270, G.271, V.272, N.320 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.272 NAG.19: 3 residues within 4Å: Chain E: H.180, P.181, N.182 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:P.181

9 x CA: CALCIUM ION(Non-covalent)

CA.5: 3 residues within 4Å: Chain A: D.185, D.186, E.252 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.186, A:E.252 CA.6: 4 residues within 4Å: Chain A: D.186, D.224, D.225, N.247 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.186, A:D.224, A:D.224, A:D.225, A:D.225 CA.7: 3 residues within 4Å: Chain A: D.292, D.293, E.359 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.292, A:D.293 CA.8: 3 residues within 4Å: Chain A: D.955, D.956, E.1022 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.955, A:D.956, A:E.1022 CA.9: 5 residues within 4Å: Chain A: S.957, D.959, V.996, K.997, C.998 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:S.957, A:D.959, A:V.996 CA.10: 5 residues within 4Å: Chain A: G.294, D.296, D.299, V.333, S.334 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:G.294, A:D.299, A:V.333 CA.12: 5 residues within 4Å: Chain B: S.747, D.749, D.752, M.786, K.787 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:S.747, B:D.752, B:D.752, B:M.786 CA.13: 4 residues within 4Å: Chain B: D.746, D.784, E.785, N.807 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.784, B:D.784, B:E.785 CA.14: 4 residues within 4Å: Chain A: E.981 Chain B: D.745, D.746, E.812 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Metal complexes: B:D.745, B:D.746, B:E.812, A:E.981

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

HEM.15: 19 residues within 4Å: Chain C: Y.43, F.44, F.47, H.59, K.62, V.63, A.66, L.67, L.84, L.87, H.88, L.92, V.94, N.98, F.99, L.102, V.133, L.137 Ligands: OXY.16 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:Y.43, C:F.44, C:F.44, C:K.62, C:K.62, C:V.63, C:A.66, C:L.84, C:L.92, C:V.94, C:F.99, C:V.133, C:L.137 Salt bridges: C:K.62, C:K.62 pi-Stacking: C:H.59 Metal complexes: C:H.88 HEM.17: 17 residues within 4Å: Chain D: T.39, F.42, F.43, H.64, K.67, V.68, A.71, L.89, L.92, H.93, L.97, N.103, F.104, L.107, V.138, L.142 Ligands: OXY.18 19 PLIP interactions: 19 interactions with chain D, Hydrophobic interactions: D:T.39, D:F.42, D:F.42, D:F.43, D:F.43, D:V.68, D:V.68, D:A.71, D:L.89, D:L.92, D:L.97, D:N.103, D:F.104, D:V.138, D:L.142 Salt bridges: D:H.64, D:K.67 pi-Stacking: D:H.64 Metal complexes: D:H.93

2 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.16: 6 residues within 4Å: Chain C: L.30, F.44, H.59, V.63, L.102 Ligands: HEM.15 No protein-ligand interaction detected (PLIP) OXY.18: 6 residues within 4Å: Chain D: L.29, F.43, H.64, V.68, L.107 Ligands: HEM.17 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, R.X. et al., Scavenger receptor CD163 multimerises to allow uptake of diverse ligands. To Be Published

Release Date

2025-07-02

Peptides

Scavenger receptor cysteine-rich type 1 protein M130: AB
Hemoglobin subunit alpha: C
Hemoglobin subunit beta: D
Isoform 2 of Haptoglobin: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

E
F

F
G

Scavenger receptor cysteine-rich type 1 protein M130

Hemoglobin subunit alpha

Hemoglobin subunit beta

Isoform 2 of Haptoglobin

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