SMTL ID : 7noz.1

Structure of the nanobody stablized properdin bound alternative pathway proconvertase C3b:FB:FP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.90 Å

Oligo State

hetero-1-1-1-1-1-1-mer

Ligands

3 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 3 residues within 4Å: Chain A: T.19, N.63, L.479 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 3 residues within 4Å: Chain B: R.186, M.187, N.188 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 1 residues within 4Å: Chain E: N.108 No protein-ligand interaction detected (PLIP)

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

FUC-BGC.3: 2 residues within 4Å: Chain C: V.123, T.124 No protein-ligand interaction detected (PLIP) FUC-BGC.4: 6 residues within 4Å: Chain C: V.64, T.65, C.66, Q.103, P.107, E.108 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:C.66 FUC-BGC.5: 3 residues within 4Å: Chain D: T.18, C.58 Chain F: R.100 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.100, F:R.100, F:R.100, F:R.100

2 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.6: 1 residues within 4Å: Chain D: N.174 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.8: 3 residues within 4Å: Chain E: N.344, E.449, R.451 No protein-ligand interaction detected (PLIP)

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

MAN.9: 4 residues within 4Å: Chain C: S.54, L.55, W.56, R.73 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.54, C:W.56, C:R.73, C:R.73 MAN.10: 2 residues within 4Å: Chain C: T.58, W.59 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:W.59, C:W.59 MAN.11: 3 residues within 4Å: Chain C: P.117, W.118, R.132 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:W.118, C:W.118, C:R.132 MAN.12: 3 residues within 4Å: Chain D: D.65, S.66, W.67 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.65, D:W.67 MAN.13: 5 residues within 4Å: Chain D: G.68, E.69, W.70, R.114, W.178 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.68, D:W.70, D:R.114, D:W.178 MAN.14: 5 residues within 4Å: Chain D: S.127, W.128, E.186, E.187, L.188 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:W.128

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

NAG.15: 2 residues within 4Å: Chain E: Y.86, N.88 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Y.86

1 x MG: MAGNESIUM ION(Non-covalent)

MG.16: 6 residues within 4Å: Chain B: N.912 Chain E: S.244, S.246, T.319, D.355, L.357 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:S.244, E:S.246, E:T.319, H2O.1, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lorentzen, J. et al., Structure determination of an unstable macromolecular complex enabled by nanobody-peptide bridging. Protein Sci. (2022)

Release Date

2022-07-27

Peptides

Complement C3 beta chain: A
Complement C3 alpha chain: B
Properdin: C
Properdin: D
Complement factor B: E
hFPNb1 nanobody: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
F

F
R

Complement C3 beta chain

Complement C3 alpha chain

Properdin

Properdin

Complement factor B

hFPNb1 nanobody

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