SMTL ID : 6f1c.1

C1rC1s complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.20 Å

Oligo State

hetero-2-2-mer

Ligands

1 x NAG- NAG- BMA- MAN- GAL- MAN: beta-D-galactopyranose-(1-4)-alpha-D-mannopyranose-(1-3)-[alpha-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-MAN-GAL-MAN.1: 3 residues within 4Å: Chain A: N.204, R.208, L.269 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.208

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-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-MAN-MAN.2: 5 residues within 4Å: Chain B: N.204, S.206, R.208, D.267, L.269 No protein-ligand interaction detected (PLIP)

2 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.3: 4 residues within 4Å: Chain C: F.148, N.159, S.161, G.162 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.148 NAG-NAG-BMA.4: 2 residues within 4Å: Chain D: F.148, N.159 No protein-ligand interaction detected (PLIP)

12 x CA: CALCIUM ION(Non-covalent)

CA.5: 7 residues within 4Å: Chain A: N.23, E.49, D.57, T.101, D.102, S.104, N.105 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.49, A:D.102, A:D.102, A:S.104 CA.6: 7 residues within 4Å: Chain A: D.125, L.126, E.128, N.150, Y.151, G.153, G.154 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.125, A:E.128, A:E.128, A:Y.151, A:G.154 CA.7: 6 residues within 4Å: Chain A: Y.197, D.226, D.236, D.273, S.275, G.276 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.226, A:D.236, A:D.273, A:D.273, A:S.275 CA.10: 8 residues within 4Å: Chain B: N.23, E.49, D.57, T.101, D.102, F.103, S.104, N.105 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.57, B:D.102 CA.11: 7 residues within 4Å: Chain B: D.125, L.126, E.128, N.150, Y.151, G.153, G.154 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.125, B:L.126, B:E.128, B:Y.151, B:G.154 CA.12: 6 residues within 4Å: Chain B: Y.197, D.226, D.236, D.273, S.275, G.276 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.226, B:D.236, B:D.273, B:D.273, B:S.275 CA.15: 7 residues within 4Å: Chain C: S.19, E.45, D.53, S.97, D.98, S.100, N.101 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.53, C:D.98, C:D.98, C:S.100 CA.17: 7 residues within 4Å: Chain C: D.116, I.117, E.119, N.134, F.135, G.137, G.138 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.116, C:I.117, C:E.119, C:F.135, C:G.138 CA.18: 6 residues within 4Å: Chain C: E.211, D.221, D.260, T.262, G.263, Q.264 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.221, C:D.260, C:G.263 CA.20: 7 residues within 4Å: Chain D: S.19, E.45, D.53, S.97, D.98, S.100, N.101 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.53, D:D.98, D:D.98, D:S.100 CA.22: 7 residues within 4Å: Chain D: D.116, I.117, E.119, N.134, F.135, G.137, G.138 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.116, D:I.117, D:E.119, D:F.135, D:G.138 CA.23: 6 residues within 4Å: Chain D: E.211, D.221, D.260, T.262, G.263, Q.264 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.221, D:D.260, D:T.262, D:G.263

6 x NA: SODIUM ION(Non-functional Binders)

NA.8: 7 residues within 4Å: Chain A: S.190, L.191, E.192, Y.193, R.195, Y.197, R.279 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.195 NA.13: 7 residues within 4Å: Chain B: S.190, L.191, E.192, Y.193, R.195, Y.197, R.279 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.191 NA.16: 7 residues within 4Å: Chain C: S.174, P.175, Y.177, K.179, P.180, Y.181, K.266 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:P.175 NA.19: 7 residues within 4Å: Chain C: S.10, P.11, N.12, Y.13, Q.15, Y.17, T.106 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.12 NA.21: 7 residues within 4Å: Chain D: S.10, P.11, N.12, Y.13, Q.15, Y.17, T.106 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.12 NA.24: 7 residues within 4Å: Chain D: S.174, P.175, Y.177, K.179, P.180, Y.181, K.266 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.266

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

NAG.9: 1 residues within 4Å: Chain A: N.108 No protein-ligand interaction detected (PLIP) NAG.14: 3 residues within 4Å: Chain B: N.108, G.109, M.112 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Almitairi, J.O.M. et al., Structure of the C1r-C1s interaction of the C1 complex of complement activation. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-01-17

Peptides

Complement C1r subcomponent: AB
Complement C1s subcomponent: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
D

D
B

Complement C1r subcomponent

Complement C1s subcomponent

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