SMTL ID : 9hek.1

Trimeric CD163 bound to human haptoglobin-haemoglobin complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-1-mer

Ligands

4 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: 2 residues within 4Å: Chain A: N.767, H.773 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: V.272, N.320, L.393 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain B: N.767, T.769, H.773 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain C: N.767, H.773 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.4: 6 residues within 4Å: Chain B: D.270, G.271, V.272, N.320, A.321, S.322 No protein-ligand interaction detected (PLIP)

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

NAG.6: 3 residues within 4Å: Chain A: L.976, F.984, N.1027 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.976 NAG.7: 2 residues within 4Å: Chain A: N.443, N.445 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.443, A:N.445 NAG.17: 4 residues within 4Å: Chain B: P.935, L.976, F.984, N.1027 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.935, B:F.984 Hydrogen bonds: B:N.1027 NAG.23: 2 residues within 4Å: Chain C: V.272, N.320 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.272 NAG.24: 4 residues within 4Å: Chain C: L.976, F.979, F.984, N.1027 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.979, C:F.984 Hydrogen bonds: C:N.1027 NAG.34: 2 residues within 4Å: Chain F: H.180, N.182 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.182

19 x CA: CALCIUM ION(Non-covalent)

CA.8: 3 residues within 4Å: Chain A: D.955, D.956, E.1022 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.955, A:E.1022 CA.9: 5 residues within 4Å: Chain A: S.747, D.749, D.752, M.786, K.787 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:S.747, A:D.749, A:D.752, A:M.786 CA.10: 6 residues within 4Å: Chain A: S.957, D.959, D.961, D.962, V.996, K.997 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:S.957, A:D.959, A:D.962, A:V.996 CA.11: 4 residues within 4Å: Chain A: D.746, D.784, E.785, N.807 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.746, A:D.784, A:E.785 CA.12: 3 residues within 4Å: Chain A: D.745, D.746, E.812 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.745, A:D.746, A:E.812 CA.13: 4 residues within 4Å: Chain A: D.185, D.186, E.252 Chain F: K.262 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.186, A:E.252 CA.14: 4 residues within 4Å: Chain A: D.186, D.224, D.225, N.247 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.186, A:D.225, A:D.225 CA.15: 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.16: 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.18: 4 residues within 4Å: Chain A: K.811 Chain B: D.955, D.956, E.1022 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.1022 CA.19: 4 residues within 4Å: Chain B: S.747, D.749, D.752, M.786 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:S.747, B:D.749, B:D.752, B:M.786 CA.20: 4 residues within 4Å: Chain B: S.957, D.959, D.962, V.996 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:S.957, B:D.959, B:D.962, B:D.962, B:V.996 CA.21: 5 residues within 4Å: Chain B: D.746, D.784, E.785, N.807 Chain C: K.1021 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.784, B:D.784 CA.22: 4 residues within 4Å: Chain B: D.745, D.746, E.812 Chain C: E.981 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.745, B:D.746, B:E.812 CA.25: 5 residues within 4Å: Chain C: S.747, D.749, D.752, M.786, K.787 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:S.747, C:D.749, C:M.786 CA.26: 4 residues within 4Å: Chain C: S.957, D.959, D.962, V.996 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:S.957, C:D.959, C:D.962, C:D.962, C:V.996 CA.27: 4 residues within 4Å: Chain C: D.746, D.784, E.785, N.807 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.746, C:D.784 CA.28: 3 residues within 4Å: Chain A: E.981 Chain C: D.746, E.812 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Metal complexes: C:E.812, A:E.981 CA.29: 3 residues within 4Å: Chain C: D.955, D.956, E.1022 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.955, C:E.1022

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

HEM.30: 17 residues within 4Å: Chain D: Y.43, F.44, F.47, H.59, K.62, V.63, A.66, L.84, L.87, H.88, L.92, V.94, N.98, F.99, L.102, L.137 Ligands: OXY.31 15 PLIP interactions: 15 interactions with chain D, Hydrophobic interactions: D:F.44, D:F.44, D:F.47, D:K.62, D:L.84, D:L.87, D:L.92, D:V.94, D:F.99, D:F.99, D:L.102, D:L.137 Salt bridges: D:K.62 pi-Stacking: D:H.59 Metal complexes: D:H.88 HEM.32: 17 residues within 4Å: Chain C: D.293, Y.354 Chain E: T.39, F.42, F.43, H.64, K.67, V.68, A.71, L.89, H.93, L.97, N.103, F.104, L.107, L.142 Ligands: OXY.33 19 PLIP interactions: 18 interactions with chain E, 1 interactions with chain C, Hydrophobic interactions: E:T.39, E:F.42, E:F.42, E:F.43, E:F.43, E:K.67, E:A.71, E:L.89, E:L.89, E:L.97, E:N.103, E:F.104, E:F.104, E:L.107, E:L.142, C:Y.354 Salt bridges: E:K.67 pi-Stacking: E:H.64 Metal complexes: E:H.93

2 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.31: 6 residues within 4Å: Chain D: L.30, F.44, H.59, V.63, L.102 Ligands: HEM.30 No protein-ligand interaction detected (PLIP) OXY.33: 6 residues within 4Å: Chain E: L.29, F.43, H.64, V.68, L.107 Ligands: HEM.32 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: ABC
Hemoglobin subunit alpha: D
Hemoglobin subunit beta: E
Isoform 2 of Haptoglobin: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
B

D
D

E
E

F
F

Scavenger receptor cysteine-rich type 1 protein M130

Hemoglobin subunit alpha

Hemoglobin subunit beta

Isoform 2 of Haptoglobin

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