SMTL ID : 8xmq.1

Structure of dimeric CD163 in complex with Hb-Hp

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-2-1-1-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: 6 residues within 4Å: Chain C: D.229, G.230, V.231, N.279, A.280, R.351 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: H.124, N.148 Ligands: NAG.3 No protein-ligand interaction detected (PLIP)

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

NAG.3: 4 residues within 4Å: Chain A: H.123, H.124, N.125 Ligands: NAG-NAG.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.123, A:N.125 NAG.4: 4 residues within 4Å: Chain A: H.180, P.181, N.182, W.339 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.181 NAG.11: 4 residues within 4Å: Chain B: D.229, G.230, V.231, N.279 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.229 NAG.12: 2 residues within 4Å: Chain B: N.402, N.404 No protein-ligand interaction detected (PLIP) NAG.13: 4 residues within 4Å: Chain B: N.726, T.728, H.732, I.776 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.776 Hydrogen bonds: B:N.726 NAG.14: 2 residues within 4Å: Chain C: N.402, N.404 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.404 NAG.15: 4 residues within 4Å: Chain C: P.894, L.935, F.943, N.986 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:P.894, C:F.943 Hydrogen bonds: C:N.986

12 x CA: CALCIUM ION(Non-covalent)

CA.5: 4 residues within 4Å: Chain A: K.94 Chain B: D.145, D.183, N.206 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.145, B:D.183, B:D.183 CA.6: 4 residues within 4Å: Chain A: K.94 Chain B: D.144, D.145, E.211 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.144, B:D.145, B:E.211 CA.7: 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.8: 4 residues within 4Å: Chain B: D.704, D.705, E.771 Chain C: K.980 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.704, B:D.705, B:E.771 CA.9: 4 residues within 4Å: Chain B: D.705, D.743, E.744, N.766 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.705, B:D.743, B:E.744 CA.10: 4 residues within 4Å: Chain B: S.706, D.708, D.711, M.745 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:S.706, B:D.708, B:D.711, B:M.745 CA.16: 3 residues within 4Å: Chain C: D.251, D.252, E.318 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.251, C:D.252, C:E.318 CA.17: 4 residues within 4Å: Chain C: D.145, D.183, D.184, N.206 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.145, C:D.183 CA.18: 3 residues within 4Å: Chain C: D.144, D.145, E.211 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.144, C:D.144, C:D.145, C:E.211 CA.19: 4 residues within 4Å: Chain B: K.770 Chain C: D.914, D.915, E.981 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.914, C:D.915, C:E.981 CA.20: 4 residues within 4Å: Chain C: H.570, D.572, D.575, F.609 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.570, C:D.572, C:D.575, C:F.609 CA.21: 6 residues within 4Å: Chain C: S.916, D.918, D.921, V.955, K.956, C.957 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:S.916, C:D.918, C:D.921, C:D.921, C:V.955

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

HEM.22: 20 residues within 4Å: Chain D: T.40, Y.43, F.44, H.46, 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 20 PLIP interactions: 20 interactions with chain D, Hydrophobic interactions: D:Y.43, D:F.44, D:F.44, D:F.44, D:V.63, D:A.66, D:L.84, D:L.92, D:V.94, D:V.94, D:N.98, D:F.99, D:L.102, D:L.102, D:V.133, D:L.137 Salt bridges: D:H.46, D:K.62 pi-Stacking: D:H.59 Metal complexes: D:H.88 HEM.23: 18 residues within 4Å: Chain E: L.32, T.39, F.42, F.43, F.46, H.64, K.67, V.68, A.71, F.72, L.89, L.92, H.93, L.97, N.103, F.104, L.107, L.142 21 PLIP interactions: 21 interactions with chain E, Hydrophobic interactions: E:L.32, E:T.39, E:F.42, E:F.42, E:F.43, E:F.43, E:F.43, E:V.68, E:V.68, E:A.71, E:F.72, E:L.89, E:L.89, E:L.92, E:L.97, E:L.142 Salt bridges: E:K.67, E:K.67 pi-Stacking: E:H.64, E:H.64 Metal complexes: E:H.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, H. et al., Structure of dimeric CD163 in complex with Hb-Hp. To Be Published

Release Date

2025-01-01

Peptides

Isoform 2 of Haptoglobin: A
Scavenger receptor cysteine-rich type 1 protein M130: BC
Hemoglobin subunit alpha: D
Hemoglobin subunit beta: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
2

B
F

C
D

D
C

E
G

Isoform 2 of Haptoglobin

Scavenger receptor cysteine-rich type 1 protein M130

Hemoglobin subunit alpha

Hemoglobin subunit beta

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