SMTL ID : 8xmp.1

Structure of CD163 in complex with Hb-Hp

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-3-1-1-mer

Ligands

3 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: 5 residues within 4Å: Chain D: D.229, G.230, V.231, N.279, R.351 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: H.124, N.148, H.149 Ligands: NAG.4 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain C: D.229, G.230, V.231, N.279 No protein-ligand interaction detected (PLIP)

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

NAG.4: 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.5: 4 residues within 4Å: Chain A: H.180, P.181, N.182, W.339 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.181, A:W.339 NAG.6: 3 residues within 4Å: Chain B: N.726, H.732, I.776 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.776 NAG.7: 5 residues within 4Å: Chain B: P.894, L.935, F.938, F.943, N.986 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.938 Hydrogen bonds: B:N.986 NAG.13: 2 residues within 4Å: Chain C: N.402, N.404 No protein-ligand interaction detected (PLIP) NAG.14: 3 residues within 4Å: Chain C: N.726, H.732, I.776 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.776 NAG.15: 4 residues within 4Å: Chain C: L.935, F.938, F.943, N.986 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.938, C:F.943 Hydrogen bonds: C:N.986 NAG.25: 1 residues within 4Å: Chain D: N.404 No protein-ligand interaction detected (PLIP) NAG.26: 2 residues within 4Å: Chain D: I.725, N.726 No protein-ligand interaction detected (PLIP) NAG.27: 5 residues within 4Å: Chain D: P.894, S.898, L.935, F.943, N.986 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:P.894, D:F.943 Hydrogen bonds: D:N.986

23 x CA: CALCIUM ION(Non-covalent)

CA.8: 4 residues within 4Å: Chain B: H.570, D.572, D.575, F.609 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.570, B:D.575, B:F.609 CA.9: 4 residues within 4Å: Chain B: D.704, D.705, E.771 Chain C: E.940 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.704, B:D.705, B:E.771 CA.10: 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.11: 5 residues within 4Å: Chain B: S.706, D.708, D.711, M.745, K.746 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:S.706, B:D.708, B:D.711, B:D.711, B:M.745 CA.12: 4 residues within 4Å: Chain B: S.916, D.918, D.921, V.955 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:S.916, B:D.918, B:D.921, B:D.921, B:V.955 CA.16: 4 residues within 4Å: Chain C: H.570, D.572, D.575, F.609 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.570, C:D.575, C:F.609 CA.17: 3 residues within 4Å: Chain C: D.704, D.705, E.771 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.704, C:D.705, C:E.771 CA.18: 4 residues within 4Å: Chain C: D.705, D.743, E.744, N.766 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.705, C:D.743, C:E.744 CA.19: 5 residues within 4Å: Chain C: S.706, D.708, D.711, M.745, K.746 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:S.706, C:D.708, C:D.711, C:D.711, C:M.745 CA.20: 5 residues within 4Å: Chain C: S.916, D.918, D.921, V.955, K.956 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 CA.21: 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.22: 4 residues within 4Å: Chain A: K.94 Chain C: D.145, D.183, N.206 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.145, C:D.183, C:D.183 CA.23: 4 residues within 4Å: Chain A: K.94 Chain C: D.144, D.145, E.211 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.144, C:D.145, C:E.211 CA.24: 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.28: 3 residues within 4Å: Chain D: D.914, D.915, E.981 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.914, D:D.915, D:E.981 CA.29: 4 residues within 4Å: Chain D: H.570, D.572, D.575, F.609 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.570, D:D.572, D:D.575, D:F.609 CA.30: 4 residues within 4Å: Chain D: S.916, D.918, D.921, V.955 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:S.916, D:D.918, D:D.921, D:D.921, D:V.955 CA.31: 3 residues within 4Å: Chain D: D.704, D.705, E.771 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.704, D:D.705, D:E.771 CA.32: 5 residues within 4Å: Chain D: S.706, D.708, D.711, M.745, K.746 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:S.706, D:D.711, D:M.745 CA.33: 6 residues within 4Å: Chain B: K.936 Chain D: D.705, D.743, E.744, N.766, C.767 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.705, D:D.743, D:E.744 CA.34: 3 residues within 4Å: Chain D: D.251, D.252, E.318 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.251, D:D.252, D:E.318 CA.35: 4 residues within 4Å: Chain D: D.145, D.183, D.184, N.206 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.145, D:D.183 CA.36: 3 residues within 4Å: Chain D: D.144, D.145, E.211 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.144, D:D.144, D:D.145, D:E.211

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

HEM.37: 20 residues within 4Å: Chain E: 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 24 PLIP interactions: 24 interactions with chain E, Hydrophobic interactions: E:Y.43, E:Y.43, E:F.44, E:F.44, E:F.44, E:V.63, E:V.63, E:A.66, E:L.67, E:L.84, E:L.92, E:L.92, E:V.94, E:V.94, E:N.98, E:F.99, E:L.102, E:L.102, E:V.133, E:L.137 Salt bridges: E:H.46, E:K.62 pi-Stacking: E:H.59 Metal complexes: E:H.88 HEM.38: 17 residues within 4Å: Chain F: L.32, T.39, F.42, F.43, 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 20 PLIP interactions: 20 interactions with chain F, Hydrophobic interactions: F:L.32, F:T.39, F:F.42, F:F.42, F:F.43, F:F.43, F:F.43, F:V.68, F:V.68, F:F.72, F:L.89, F:L.92, F:L.97, F:F.104, F:F.104, F:L.142 Salt bridges: F:K.67, F:K.67 pi-Stacking: F:H.64 Metal complexes: F:H.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, H. et al., Structure of 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: BCD
Hemoglobin subunit alpha: E
Hemoglobin subunit beta: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
2

B
E

C
F

D
D

E
C

F
G

Isoform 2 of Haptoglobin

Scavenger receptor cysteine-rich type 1 protein M130

Hemoglobin subunit alpha

Hemoglobin subunit beta

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