SMTL ID : 6cxo.3 (2 other biounits)

Complement component-9

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

10 x ZN: ZINC ION(Non-covalent)

ZN.1: 2 residues within 4Å: Chain A: D.195, H.197 No protein-ligand interaction detected (PLIP) ZN.6: 3 residues within 4Å: Chain A: H.358, F.362, N.363 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.358 ZN.7: 2 residues within 4Å: Chain A: H.526 Chain C: H.526 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: A:H.526, C:H.526, H2O.21 ZN.8: 2 residues within 4Å: Chain B: D.195, H.197 No protein-ligand interaction detected (PLIP) ZN.13: 3 residues within 4Å: Chain B: H.358, F.362, N.363 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.358 ZN.14: 2 residues within 4Å: Chain B: H.526 Chain D: H.526 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: D:H.526, B:H.526, H2O.26 ZN.15: 3 residues within 4Å: Chain C: D.195, E.196, H.197 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.197 ZN.20: 3 residues within 4Å: Chain C: H.358, F.362, N.363 No protein-ligand interaction detected (PLIP) ZN.21: 3 residues within 4Å: Chain D: D.195, E.196, H.197 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.197 ZN.26: 3 residues within 4Å: Chain D: H.358, F.362, N.363 No protein-ligand interaction detected (PLIP)

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: L.96, N.99, D.101, D.103, D.109, E.110 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:L.96, A:D.101, A:D.103, A:D.109, A:E.110 CA.9: 6 residues within 4Å: Chain B: L.96, N.99, D.101, D.103, D.109, E.110 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:L.96, B:D.101, B:D.103, B:D.109, B:E.110 CA.16: 6 residues within 4Å: Chain C: L.96, N.99, D.101, D.103, D.109, E.110 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:L.96, C:D.101, C:D.103, C:D.109, C:E.110 CA.22: 6 residues within 4Å: Chain D: L.96, N.99, D.101, D.103, D.109, E.110 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:L.96, D:D.101, D:D.103, D:D.109, D:E.110

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

NAG.3: 7 residues within 4Å: Chain A: H.197, L.198, G.500, T.502, S.513, C.514 Chain B: K.347 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:H.197, A:T.502, B:K.347, B:K.347 Water bridges: A:L.198 NAG.10: 7 residues within 4Å: Chain A: K.347 Chain B: H.197, L.198, G.500, T.502, S.513, C.514 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:H.197, B:T.502, A:K.347, A:K.347 Water bridges: B:L.198 NAG.17: 7 residues within 4Å: Chain C: L.198, G.500, T.502, S.513, C.514, P.515 Chain D: K.347 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.502, C:C.514 NAG.23: 7 residues within 4Å: Chain C: K.347 Chain D: L.198, G.500, T.502, S.513, C.514, P.515 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.502, D:C.514 Water bridges: D:E.196

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 2 residues within 4Å: Chain A: N.205, D.215 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain B: N.205, D.215 No protein-ligand interaction detected (PLIP) MG.18: 3 residues within 4Å: Chain C: S.210, N.213, D.215 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.210, C:N.213, C:D.215, H2O.18, H2O.19 MG.24: 3 residues within 4Å: Chain D: S.210, N.213, D.215 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:S.210, D:N.213, D:D.215, H2O.23, H2O.24

4 x BMA: beta-D-mannopyranose(Post Translational Modification)

BMA.5: 3 residues within 4Å: Chain A: P.26, W.27, R.42 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.27, A:R.42, A:R.42 Water bridges: A:S.25 BMA.12: 3 residues within 4Å: Chain B: P.26, W.27, R.42 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:W.27, B:R.42, B:R.42 Water bridges: B:S.25 BMA.19: 3 residues within 4Å: Chain C: P.26, W.27, R.42 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:W.27, C:W.27, C:R.42, C:R.42 BMA.25: 3 residues within 4Å: Chain D: P.26, W.27, R.42 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:W.27, D:W.27, D:R.42, D:R.42

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Spicer, B.A. et al., The first transmembrane region of complement component-9 acts as a brake on its self-assembly. Nat Commun (2018)

Release Date

2018-09-05

Peptides

Complement component C9: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
A

D
A

Complement component C9

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