SMTL ID : 5o32.1

The structure of complement complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.21 Å

Oligo State

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

Ligands

2 x NAG- NAG- BMA- BMA- BMA: beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-BMA-BMA.1: 6 residues within 4Å: Chain A: T.19, N.63, L.478, L.479, K.480, A.481 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.480 NAG-NAG-BMA-BMA-BMA.3: 6 residues within 4Å: Chain F: T.19, N.63, L.478, L.479, K.480, A.481 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:K.480

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

NAG-NAG.2: 3 residues within 4Å: Chain A: N.178 Chain B: N.191, T.193 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain F: N.178 Chain G: N.191 No protein-ligand interaction detected (PLIP)

6 x CA: CALCIUM ION(Non-covalent)

CA.5: 5 residues within 4Å: Chain A: P.505, D.532, V.533, D.535, E.599 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.532, A:D.535 CA.6: 6 residues within 4Å: Chain D: Y.258, N.261, E.263, D.265, D.271, E.272 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:Y.258, D:E.263, D:D.265, D:D.271, D:E.272 CA.7: 8 residues within 4Å: Chain D: K.221, A.222, C.223, D.224, I.226, D.228, D.234, E.235 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.224, D:I.226, D:D.228, D:D.234, D:E.235 CA.14: 5 residues within 4Å: Chain F: P.505, D.532, V.533, D.535, E.599 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.532, F:D.535 CA.15: 6 residues within 4Å: Chain I: Y.258, N.261, E.263, D.265, D.271, E.272 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:Y.258, I:E.263, I:D.265, I:D.271, I:E.272 CA.16: 8 residues within 4Å: Chain I: K.221, A.222, C.223, D.224, I.226, D.228, D.234, E.235 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:K.221, I:D.224, I:I.226, I:D.228, I:D.234

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

NAG.8: 3 residues within 4Å: Chain D: N.52, R.299 Ligands: NAG.17 No protein-ligand interaction detected (PLIP) NAG.9: 1 residues within 4Å: Chain D: N.159 No protein-ligand interaction detected (PLIP) NAG.10: 4 residues within 4Å: Chain D: T.54, N.85, A.291, E.296 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.54, D:E.296 NAG.11: 3 residues within 4Å: Chain E: D.194, A.195, N.197 No protein-ligand interaction detected (PLIP) NAG.12: 2 residues within 4Å: Chain E: N.125, K.151 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:K.151 NAG.13: 2 residues within 4Å: Chain E: N.155, S.157 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.155 NAG.17: 3 residues within 4Å: Chain I: N.52, R.299 Ligands: NAG.8 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:R.299 NAG.18: 1 residues within 4Å: Chain I: N.159 No protein-ligand interaction detected (PLIP) NAG.19: 3 residues within 4Å: Chain I: T.54, N.85, A.291 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:T.54 Hydrogen bonds: I:T.54 NAG.20: 2 residues within 4Å: Chain J: A.195, N.197 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:N.197 NAG.21: 2 residues within 4Å: Chain J: N.125, K.151 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:K.151 NAG.22: 2 residues within 4Å: Chain J: N.155, K.158 No protein-ligand interaction detected (PLIP)

1 x MLI: MALONATE ION(Non-functional Binders)

MLI.23: 3 residues within 4Å: Chain E: R.109 Chain J: K.66, R.109 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain J Salt bridges: E:R.109, E:R.109, J:K.66, J:R.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xue, X. et al., Regulator-dependent mechanisms of C3b processing by factor I allow differentiation of immune responses. Nat. Struct. Mol. Biol. (2017)

Release Date

2017-06-28

Peptides

Complement C3: AF
Complement C3: BG
Complement factor H,Complement factor H: CH
Complement factor I: DI
Complement factor I: EJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
E

B
B

G
F

C
C

H
G

D
D

I
H

E
I

J
J

Complement C3

Complement C3

Complement factor H,Complement factor H

Complement factor I

Complement factor I

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