SMTL ID : 9fhb.1

Cryo-EM structure of human CD163 SRCR2-4 in complex with haptoglobin-hemoglobin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

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

HEM.1: 17 residues within 4Å: Chain A: M.33, Y.43, F.44, H.59, K.62, V.63, A.66, L.84, L.87, H.88, L.92, V.94, N.98, F.99, L.102, V.133, L.137 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:Y.43, A:F.44, A:F.44, A:K.62, A:V.63, A:V.63, A:A.66, A:L.87, A:L.92, A:V.94, A:N.98, A:F.99, A:L.102, A:V.133, A:L.137 Salt bridges: A:K.62, A:K.62 Metal complexes: A:H.88 HEM.2: 16 residues within 4Å: Chain B: T.39, F.42, F.43, H.64, K.67, V.68, A.71, F.72, L.89, L.92, H.93, L.97, V.99, F.104, L.107, L.142 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:T.39, B:F.42, B:F.43, B:V.68, B:F.72, B:L.89, B:L.97, B:V.99, B:F.104, B:L.142 pi-Stacking: B:H.64, B:H.93 Metal complexes: B:H.93

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

NAG.3: 2 residues within 4Å: Chain C: H.182, N.184 No protein-ligand interaction detected (PLIP) NAG.4: 2 residues within 4Å: Chain C: H.239, N.241 No protein-ligand interaction detected (PLIP) NAG.7: 1 residues within 4Å: Chain D: N.320 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.320, D:N.320

2 x CA: CALCIUM ION(Non-covalent)

CA.5: 5 residues within 4Å: Chain D: D.186, D.224, D.225, N.247, C.248 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.186, D:D.224, D:D.224, D:D.225 CA.6: 5 residues within 4Å: Chain D: G.294, D.296, D.299, V.333, S.334 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:G.294, D:D.299, D:V.333

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Etzerodt, E. et al., The structure of human scavenger receptor CD163 in complex with haptoglobin-hemoglobin discloses the molecular mechanism for hemoglobin scavenging. To Be Published

Release Date

2024-12-18

Peptides

Hemoglobin subunit alpha: A
Hemoglobin subunit beta: B
Haptoglobin: C
Scavenger receptor cysteine-rich type 1 protein M130: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Hemoglobin subunit alpha

Hemoglobin subunit beta

Haptoglobin

Scavenger receptor cysteine-rich type 1 protein M130

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