SMTL ID : 7ue9.1

Structure of anti-C3d Fab(3d8b) in complex with C3d

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

hetero-1-1-1-mer

Ligands

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 11 residues within 4Å: Chain A: Q.187, S.189, S.203, S.204, T.205 Chain B: F.183, P.184, V.186, S.194, L.195, S.196 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.187, A:S.189, A:T.205, B:F.183, B:S.194, B:S.196 GOL.2: 6 residues within 4Å: Chain A: T.191, E.192, Q.193, D.194 Chain B: V.180, H.181 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.194, A:D.194, B:V.180 Water bridges: A:E.192, B:T.182, B:T.182 GOL.3: 5 residues within 4Å: Chain A: V.177, Q.182, N.185, L.208, H.216 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.185 Water bridges: A:H.216 GOL.4: 5 residues within 4Å: Chain A: N.185, S.186, Q.187 Chain B: Q.188, S.189 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.185, B:S.189, B:S.189 Water bridges: A:Q.187, B:S.190 GOL.5: 7 residues within 4Å: Chain B: R.57, Q.58, A.59, Q.62, G.63, L.64, E.65 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.57, B:A.59, B:G.63, B:L.64 GOL.6: 3 residues within 4Å: Chain B: T.49, N.50, Y.73 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.50 Water bridges: B:N.71 GOL.7: 7 residues within 4Å: Chain C: S.83, W.85, E.128, P.131, V.132, Q.135, I.138 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.83, C:E.128, C:V.132, C:Q.135 GOL.8: 6 residues within 4Å: Chain C: E.229, D.230, P.231, G.232, Q.234, N.237 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.229, C:G.232, C:G.232 GOL.9: 9 residues within 4Å: Chain C: V.3, L.264, N.265, Q.267, R.268, Y.269, Y.270, F.284, L.287 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.265, C:Y.269, C:Y.269 GOL.10: 3 residues within 4Å: Chain C: L.308, P.309, S.310 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.310, C:S.310

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fahnoe, K.C. et al., Development and Optimization of Bifunctional Fusion Proteins to Locally Modulate Complement Activation in Diseased Tissue. Front Immunol (2022)

Release Date

2022-06-08

Peptides

Fab light chain: A
Fab heavy chain: B
Complement C3dg fragment: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

C
C

Fab light chain

Fab heavy chain

Complement C3dg fragment