SMTL ID : 8q6r.1 (1 other biounit)

Structure of complement FP in complex with the TPP-3077 VHH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x FUC- BGC: beta-D-glucopyranose-(1-3)-alpha-L-fucopyranose(Post Translational Modification)

FUC-BGC.1: 6 residues within 4Å: Chain B: V.64, T.65, C.66, Q.103, C.106, P.107 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.65 FUC-BGC.2: 8 residues within 4Å: Chain A: V.54 Chain B: N.32, A.34 Chain C: V.17, T.18, C.19, C.58, P.59 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.32 Water bridges: B:N.32, B:A.34

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 1 residues within 4Å: Chain C: N.174 No protein-ligand interaction detected (PLIP)

2 x GCH: GLYCOCHOLIC ACID(Non-covalent)

GCH.4: 6 residues within 4Å: Chain A: V.92, Q.111, G.112, T.113, L.114 Ligands: GCH.5 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.111 GCH.5: 10 residues within 4Å: Chain A: Q.39, A.40, P.41, T.90, A.91, V.92, L.114, T.116, S.118 Ligands: GCH.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.41 Hydrogen bonds: A:A.40, A:S.118

10 x MAN: alpha-D-mannopyranose(Post Translational Modification)

MAN.6: 4 residues within 4Å: Chain B: L.55, W.56, R.73, R.75 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.56, B:R.73, B:R.73 MAN.7: 5 residues within 4Å: Chain B: S.57, T.58, W.59, Q.71, R.73 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.57, B:T.58, B:T.58, B:W.59 Water bridges: B:Q.71, B:Q.71 MAN.8: 5 residues within 4Å: Chain A: D.61, K.64 Chain C: E.63, W.64, R.94 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:W.64, C:R.94, C:R.94, A:D.61, A:K.64 Water bridges: C:A.107, C:A.107, A:D.61 MAN.9: 3 residues within 4Å: Chain C: S.66, W.67, R.92 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:W.67, C:R.92, C:R.92 Water bridges: C:D.65 MAN.10: 5 residues within 4Å: Chain C: G.68, E.69, W.70, R.114, W.178 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:G.68, C:E.69, C:W.70, C:R.114, C:R.114 Water bridges: C:W.70, C:W.70 MAN.11: 5 residues within 4Å: Chain C: S.127, W.128, C.185, E.186, L.188 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:W.128, C:E.186 MAN.12: 4 residues within 4Å: Chain B: A.99 Chain C: T.133, W.134, R.147 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:W.134, C:R.147, C:R.147 Water bridges: C:S.132 MAN.13: 4 residues within 4Å: Chain C: E.130, W.131, R.149, R.151 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.130, C:W.131, C:R.149, C:R.149 MAN.14: 5 residues within 4Å: Chain C: G.5, W.6, R.28, C.42, A.43 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:W.6, C:R.28, C:R.28 MAN.15: 4 residues within 4Å: Chain C: G.7, P.8, W.9, R.48 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.7, C:W.9, C:R.48, C:R.48

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tamburini, P. et al., Characterization of the bispecific VHH antibody tarperprumig (ALXN1820) specific for properdin and designed for low-volume administration. Mabs (2024)

Release Date

2024-08-28

Peptides

The properdin specific VHH TPP-3077: A
Properdin: B
Properdin: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
D

The properdin specific VHH TPP-3077

Properdin

Properdin

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