SMTL ID : 6rur.1

Structure of the SCIN stabilized C3bBb convertase bound to properdin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 6.00 Å

Oligo State

hetero-2-2-2-2-2-2-mer

Ligands

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

FUC-BGC.1: 3 residues within 4Å: Chain A: T.65, C.66, C.106 No protein-ligand interaction detected (PLIP) FUC-BGC.2: 4 residues within 4Å: Chain B: V.17, T.18, C.58, P.59 No protein-ligand interaction detected (PLIP) FUC-BGC.4: 3 residues within 4Å: Chain C: T.65, C.66, C.106 No protein-ligand interaction detected (PLIP) FUC-BGC.5: 5 residues within 4Å: Chain C: N.32 Chain D: V.17, T.18, C.58, P.59 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.32

2 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.3: 1 residues within 4Å: Chain B: N.174 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.6: 1 residues within 4Å: Chain D: N.174 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.7: 2 residues within 4Å: Chain E: N.63, A.481 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain E: N.178 Chain F: N.191 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain G: N.63, K.480, A.481 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain G: P.148, E.149, N.178 Chain H: N.191 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:P.148 NAG-NAG.11: 3 residues within 4Å: Chain I: S.25, N.26, P.173 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain I: W.118, N.119 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain J: S.25, N.26, P.173, V.196 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain J: W.118, N.119 No protein-ligand interaction detected (PLIP)

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

MAN.15: 4 residues within 4Å: Chain A: S.54, L.55, W.56, R.73 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.54, A:W.56, A:R.73, A:R.73 MAN.16: 2 residues within 4Å: Chain A: T.58, W.59 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.57, A:T.58, A:T.58, A:W.59 MAN.17: 4 residues within 4Å: Chain B: D.65, S.66, W.67, R.92 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.65, B:W.67, B:R.92, B:R.92 MAN.18: 5 residues within 4Å: Chain B: G.68, E.69, W.70, R.114, W.178 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.70, B:W.70, B:R.114 MAN.19: 4 residues within 4Å: Chain B: S.127, W.128, R.151, E.186 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.127, B:W.128, B:W.128, B:R.151, B:E.186, B:E.186 MAN.20: 4 residues within 4Å: Chain B: S.132, T.133, W.134, R.147 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.132, B:W.134, B:R.147 MAN.21: 2 residues within 4Å: Chain B: E.130, W.131 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.130, B:E.130, B:W.131, B:W.131, B:R.149 MAN.22: 6 residues within 4Å: Chain B: G.5, W.6, R.28, C.42, A.43 Ligands: MAN.23 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:W.6, B:R.28, B:R.28, B:C.42 MAN.23: 5 residues within 4Å: Chain B: G.7, P.8, W.9, R.48 Ligands: MAN.22 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.9, B:W.9, B:R.48 MAN.24: 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:W.56, C:W.56, C:R.73, C:R.73 MAN.25: 2 residues within 4Å: Chain C: T.58, W.59 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.57, C:T.58, C:T.58, C:W.59 MAN.26: 4 residues within 4Å: Chain D: D.65, S.66, W.67, R.92 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.65, D:W.67, D:R.92, D:R.92 MAN.27: 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:W.70, D:W.70, D:R.114, D:W.178 MAN.28: 6 residues within 4Å: Chain D: G.126, S.127, W.128, R.151, C.185, E.186 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.127, D:W.128, D:W.128, D:R.151, D:E.186, D:E.186 MAN.29: 4 residues within 4Å: Chain D: S.132, T.133, W.134, R.147 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.132, D:W.134, D:R.147 MAN.30: 3 residues within 4Å: Chain D: E.130, W.131, R.149 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:W.131, D:W.131, D:R.149, D:R.149 MAN.31: 6 residues within 4Å: Chain D: G.5, W.6, R.28, C.42, A.43 Ligands: MAN.32 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:W.6, D:R.28, D:R.28, D:C.42 MAN.32: 5 residues within 4Å: Chain D: G.7, P.8, W.9, R.48 Ligands: MAN.31 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.7, D:W.9, D:R.48, D:R.48

2 x MG: MAGNESIUM ION(Non-covalent)

MG.33: 6 residues within 4Å: Chain F: N.915 Chain J: D.17, S.19, S.21, T.94, D.130 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain F Metal complexes: J:S.19, J:S.21, J:T.94, F:N.915 MG.34: 6 residues within 4Å: Chain H: N.915 Chain I: D.17, S.19, S.21, T.94, D.130 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:S.19, I:S.21, I:T.94

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pedersen, D.V. et al., Structural Basis for Properdin Oligomerization and Convertase Stimulation in the Human Complement System. Front Immunol (2019)

Release Date

2019-08-21

Peptides

Properdin: AC
Properdin: BD
Complement C3: EG
Complement C3: FH
Complement factor B: IJ
Inhibitor: KL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
U

C
X

B
V

D
Y

E
A

G
G

F
B

H
H

I
J

J
L

K
N

L
Q

Properdin

Properdin

Complement C3

Complement C3

Complement factor B

Inhibitor

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