SMTL ID : 9fmu.1

Cryo-EM structure of human CD163 SRCR1-9 in complex with haptoglobin-hemoglobin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-2-mer

Ligands

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.1: 12 residues within 4Å: Chain A: Y.43, F.44, F.47, H.59, K.62, V.63, L.84, H.88, L.92, V.94, N.98, L.102 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:F.44, A:F.47, A:K.62, A:K.62, A:V.63, A:L.84, A:L.84, A:L.92, A:V.94, A:N.98 Salt bridges: A:K.62, A:K.62 pi-Cation interactions: A:H.59 Metal complexes: A:H.88 HEM.2: 12 residues within 4Å: Chain B: F.42, F.43, H.64, K.67, V.68, L.89, L.92, H.93, L.97, V.99, F.104, L.107 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:F.42, B:F.42, B:F.43, B:F.43, B:K.67, B:V.68, B:L.89, B:L.92, B:L.97, B:V.99, B:F.104, B:L.107 pi-Cation interactions: B:H.93 Metal complexes: B:H.93

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

NAG.3: 2 residues within 4Å: Chain C: H.123, N.125 No protein-ligand interaction detected (PLIP) NAG.4: 3 residues within 4Å: Chain C: H.180, P.181, N.182 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:P.181 Hydrogen bonds: C:N.182 NAG.7: 2 residues within 4Å: Chain D: V.272, N.320 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.270 NAG.8: 4 residues within 4Å: Chain D: P.935, L.976, K.977, N.1027 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.977 NAG.10: 2 residues within 4Å: Chain E: I.766, N.767 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.767

3 x CA: CALCIUM ION(Non-covalent)

CA.5: 4 residues within 4Å: Chain D: D.186, D.224, D.225, N.247 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.186, D:D.224, D:D.224, D:D.225, D:D.225 CA.6: 6 residues within 4Å: Chain D: G.294, W.295, 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 CA.9: 5 residues within 4Å: Chain E: G.294, D.296, D.299, V.333, S.334 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:G.294, E:D.299, E:V.333

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Etzerodt, A. et al., The Cryo-EM structure of human CD163 bound to haptoglobin-hemoglobin reveals molecular mechanisms of hemoglobin scavenging. Nat Commun (2024)

Release Date

2024-12-18

Peptides

Hemopressin: A
Spinorphin: B
Isoform 2 of Haptoglobin: C
Scavenger receptor cysteine-rich type 1 protein M130: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Hemopressin

Spinorphin

Isoform 2 of Haptoglobin

Scavenger receptor cysteine-rich type 1 protein M130

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