SMTL ID : 6ruv.1

Structure of the SCIN stabilized C3bBb convertase bound to Properdin and a the non-inhibitory nanobody hFPNb1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 6.15 Å

Oligo State

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

Ligands

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

FUC-BGC.1: 1 residues within 4Å: Chain C: T.65 No protein-ligand interaction detected (PLIP) FUC-BGC.2: 6 residues within 4Å: Chain B: R.101 Chain C: N.32 Chain D: V.17, T.18, C.58, P.59 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: C:N.32, B:R.101, D:T.18 FUC-BGC.4: 4 residues within 4Å: Chain E: V.123, T.124, C.125, C.163 No protein-ligand interaction detected (PLIP) FUC-BGC.5: 5 residues within 4Å: Chain E: V.64, T.65, C.66, C.106, P.107 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:P.107 FUC-BGC.6: 6 residues within 4Å: Chain A: R.101 Chain E: N.32 Chain F: V.17, T.18, C.58, P.59 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:N.32, A:R.101, A:R.101

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 D: N.174 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.7: 1 residues within 4Å: Chain F: 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.8: 3 residues within 4Å: Chain G: N.63, K.480, A.481 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain G: E.149, N.178 Chain H: N.191 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain I: N.63, K.480, A.481 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain I: E.149, N.178 Chain J: N.191 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain K: S.25, N.26, P.173, V.196 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain K: W.118, N.119 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain L: S.25, N.26, P.173, V.196 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain L: W.118, N.119 No protein-ligand interaction detected (PLIP)

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

MAN.16: 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.17: 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.18: 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.19: 6 residues within 4Å: Chain D: G.68, E.69, W.70, R.114, W.178, G.179 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.68, D:W.70, D:R.114, D:G.179 MAN.20: 3 residues within 4Å: Chain D: S.127, W.128, R.151 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.127, D:W.128, D:W.128, D:R.151, D:R.151 MAN.21: 4 residues within 4Å: Chain D: S.132, T.133, W.134, R.147 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.132, D:W.134, D:R.147, D:R.147 MAN.22: 3 residues within 4Å: Chain D: E.130, W.131, R.149 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:E.130, D:E.130, D:W.131, D:W.131, D:R.149, D:R.149 MAN.23: 5 residues within 4Å: Chain D: G.5, W.6, R.28, C.42 Ligands: MAN.24 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:W.6, D:R.28, D:R.28, D:C.42 MAN.24: 5 residues within 4Å: Chain D: G.7, P.8, W.9, R.48 Ligands: MAN.23 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.7, D:W.9, D:R.48 MAN.25: 4 residues within 4Å: Chain E: S.54, L.55, W.56, R.73 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:W.56, E:W.56, E:R.73, E:R.73 MAN.26: 2 residues within 4Å: Chain E: T.58, W.59 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:S.57, E:T.58, E:W.59 MAN.27: 4 residues within 4Å: Chain E: G.111, W.112, R.134, P.148 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:W.112, E:W.112, E:R.134, E:R.134 MAN.28: 4 residues within 4Å: Chain E: S.113, G.114, W.115, R.132 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:S.113, E:W.115, E:R.132, E:R.132 MAN.29: 4 residues within 4Å: Chain E: G.116, P.117, W.118, R.130 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:W.118, E:W.118, E:R.130 MAN.30: 4 residues within 4Å: Chain F: D.65, S.66, W.67, R.92 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:D.65, F:W.67, F:R.92, F:R.92 MAN.31: 6 residues within 4Å: Chain F: G.68, E.69, W.70, R.114, W.178, G.179 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:G.68, F:W.70, F:R.114, F:W.178, F:G.179 MAN.32: 4 residues within 4Å: Chain F: G.126, S.127, W.128, C.185 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:S.127, F:W.128, F:W.128 MAN.33: 4 residues within 4Å: Chain F: S.132, T.133, W.134, R.147 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:S.132, F:W.134, F:R.147, F:R.147 MAN.34: 3 residues within 4Å: Chain F: E.130, W.131, R.149 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:E.130, F:W.131, F:W.131, F:R.149, F:R.149 MAN.35: 5 residues within 4Å: Chain F: G.5, W.6, R.28, C.42 Ligands: MAN.36 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:W.6, F:R.28, F:R.28, F:C.42 MAN.36: 4 residues within 4Å: Chain F: G.7, P.8, W.9 Ligands: MAN.35 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:W.9, F:W.9

2 x MG: MAGNESIUM ION(Non-covalent)

MG.37: 6 residues within 4Å: Chain J: N.915 Chain K: D.17, S.19, S.21, T.94, D.130 4 PLIP interactions: 3 interactions with chain K, 1 interactions with chain J Metal complexes: K:S.19, K:S.21, K:T.94, J:N.915 MG.38: 6 residues within 4Å: Chain H: N.915 Chain L: D.17, S.19, S.21, T.94, D.130 4 PLIP interactions: 3 interactions with chain L, 1 interactions with chain H Metal complexes: L:S.19, L:S.21, L:T.94, H:N.915

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

Nanobody hFPNb1: AB
Properdin: CE
Properdin: DF
Complement C3: GI
Complement C3: HJ
Complement factor B: KL
Inhibitor: MN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
R

B
S

C
U

E
X

D
V

F
Y

G
A

I
G

H
B

J
H

K
J

L
L

M
N

N
Q

Nanobody hFPNb1

Properdin

Properdin

Complement C3

Complement C3

Complement factor B

Inhibitor

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