SMTL ID : 8a59.1

C-type lectin-like domain (CTLD) and Sushi-like domain of human CD93

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

homo-dimer

Ligands

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: S.47, K.48, E.49, P.106 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.48, A:E.49 Water bridges: A:E.49, A:P.106 GOL.2: 4 residues within 4Å: Chain A: S.47, E.49, E.50, H.53 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.47, A:S.47, A:H.53 Water bridges: A:Y.19, A:Y.19, A:E.49 GOL.3: 4 residues within 4Å: Chain A: K.85, C.86, L.87, D.88 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.86 Water bridges: A:K.85, A:C.86 GOL.4: 3 residues within 4Å: Chain A: L.114, R.115, N.116 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.116 GOL.5: 4 residues within 4Å: Chain A: F.220, L.221, K.223, W.232 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.221, A:K.223, A:K.223 GOL.6: 4 residues within 4Å: Chain A: P.92, P.106, Y.107, S.108 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.108 GOL.10: 4 residues within 4Å: Chain B: S.47, K.48, E.49, P.106 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.48, B:E.49 Water bridges: B:S.47, B:P.106 GOL.11: 4 residues within 4Å: Chain B: S.47, E.49, E.50, H.53 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.47, B:S.47, B:H.53 Water bridges: B:E.50 GOL.12: 4 residues within 4Å: Chain B: K.85, C.86, L.87, D.88 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:C.86 Water bridges: B:K.85, B:C.86 GOL.13: 3 residues within 4Å: Chain B: L.114, R.115, N.116 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.116 GOL.14: 4 residues within 4Å: Chain B: F.220, L.221, K.223, W.232 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.221, B:K.223, B:K.223 GOL.15: 4 residues within 4Å: Chain B: P.92, P.106, Y.107, S.108 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.108

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 3 residues within 4Å: Chain A: R.122, G.145, P.146 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.115, A:R.122 SO4.8: 7 residues within 4Å: Chain A: K.74, W.76, S.125, G.145, P.146, S.155, I.157 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.123, A:S.125 Salt bridges: A:K.74 SO4.9: 7 residues within 4Å: Chain A: Q.60, R.63, R.64 Chain B: Q.60, R.63, R.64 Ligands: SO4.18 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Salt bridges: B:R.63, B:R.64, A:R.63, A:R.64 SO4.16: 3 residues within 4Å: Chain B: R.122, G.145, P.146 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.115, B:R.122 SO4.17: 7 residues within 4Å: Chain B: K.74, W.76, S.125, G.145, P.146, S.155, I.157 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:C.123, B:S.125 Salt bridges: B:K.74 SO4.18: 7 residues within 4Å: Chain A: Q.60, R.63, R.64 Chain B: Q.60, R.63, R.64 Ligands: SO4.9 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Salt bridges: A:R.63, A:R.64, B:R.63, B:R.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barbera, S. et al., Dimerization of the C-type lectin-like receptor CD93 promotes its binding to Multimerin-2 in endothelial cells. Int.J.Biol.Macromol. (2023)

Release Date

2022-11-02

Peptides

Complement component C1q receptor: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Complement component C1q receptor