SMTL ID : 2qki.2 (1 other biounit)

Human C3c in complex with the inhibitor compstatin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

NAG-NAG.1: 7 residues within 4Å: Chain A: T.19, N.63, L.478, L.479, K.480, A.481 Ligands: BR.16 No protein-ligand interaction detected (PLIP)

3 x K: POTASSIUM ION(Non-covalent)

K.2: 4 residues within 4Å: Chain A: P.505, D.532, V.533, D.535 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:P.505, A:D.532, A:V.533, A:D.535 K.3: 3 residues within 4Å: Chain A: R.13, K.475, A.601 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:A.601 K.31: 3 residues within 4Å: Chain C: A.102, G.104, R.107 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:A.102, C:G.104, C:R.107

20 x BR: BROMIDE ION(Non-covalent)(Non-functional Binders)

BR.4: 4 residues within 4Å: Chain A: G.476, D.602, I.603, G.604 Ligand excluded by PLIP BR.5: 4 residues within 4Å: Chain A: N.147, V.177, N.178, W.182 Ligand excluded by PLIP BR.6: 5 residues within 4Å: Chain A: K.337, R.508, T.606, P.607 Ligands: GOL.24 Ligand excluded by PLIP BR.7: 5 residues within 4Å: Chain A: D.535, S.536, Q.591, W.595 Ligands: GOL.29 Ligand excluded by PLIP BR.8: 3 residues within 4Å: Chain A: K.464, L.515, I.516 Ligand excluded by PLIP BR.9: 3 residues within 4Å: Chain A: P.445, T.500, T.501 Ligand excluded by PLIP BR.10: 3 residues within 4Å: Chain A: K.267, V.278, V.279 Ligand excluded by PLIP BR.11: 3 residues within 4Å: Chain A: N.59, Y.467, R.483 Ligand excluded by PLIP BR.12: 3 residues within 4Å: Chain A: D.458, R.459 Chain D: D.7 Ligand excluded by PLIP BR.13: 4 residues within 4Å: Chain A: P.366, K.406, Q.407, E.408 Ligand excluded by PLIP BR.14: 3 residues within 4Å: Chain A: N.162, Q.163, L.164 Ligand excluded by PLIP BR.15: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP BR.16: 3 residues within 4Å: Chain A: G.62, N.63 Ligands: NAG-NAG.1 Ligand excluded by PLIP BR.17: 3 residues within 4Å: Chain A: N.81, E.637, L.638 Ligand excluded by PLIP BR.18: 2 residues within 4Å: Chain A: Q.557, Q.558 Ligand excluded by PLIP BR.26: 6 residues within 4Å: Chain B: T.129, K.131, R.132 Chain C: E.196, N.197, K.304 Ligand excluded by PLIP BR.27: 2 residues within 4Å: Chain B: E.18, P.20 Ligand excluded by PLIP BR.28: 2 residues within 4Å: Chain B: I.45, F.46 Ligand excluded by PLIP BR.32: 4 residues within 4Å: Chain B: S.147 Chain C: D.120, N.122, T.123 Ligand excluded by PLIP BR.33: 4 residues within 4Å: Chain C: G.104, V.105, D.106, R.107 Ligand excluded by PLIP

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.19: 6 residues within 4Å: Chain A: S.105, R.139, T.140, Y.188, E.189, N.190 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.105, A:S.105, A:T.140, A:T.140, A:E.189, A:N.190 Water bridges: A:T.140 GOL.20: 6 residues within 4Å: Chain A: S.536, C.537, V.538, G.539, S.540 Ligands: GOL.29 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.537 GOL.21: 4 residues within 4Å: Chain A: G.240, K.241, K.242 Chain B: K.143 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.240, A:K.242, B:K.143 GOL.22: 5 residues within 4Å: Chain A: E.218, F.220, Y.222, P.330, E.413 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.413 GOL.23: 7 residues within 4Å: Chain A: R.13, S.16, S.105, N.131, H.132, K.133, K.475 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.13, A:S.16, A:S.105, A:H.132, A:K.133, A:K.133, A:K.475 Water bridges: A:E.17 GOL.24: 8 residues within 4Å: Chain A: R.508, E.599, K.600, D.602, G.604, C.605, C.640 Ligands: BR.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.602, A:D.602 GOL.25: 3 residues within 4Å: Chain A: E.320, R.321, S.322 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.322, A:S.322 GOL.29: 10 residues within 4Å: Chain A: S.536, C.537, L.541, Q.591 Chain B: V.69, A.70, D.71 Ligands: BR.7, GOL.20, GOL.30 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:C.537, A:L.541 Water bridges: B:D.71 GOL.30: 8 residues within 4Å: Chain A: L.589, T.590, Q.591 Chain B: L.57, V.69, A.70, P.72 Ligands: GOL.29 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.591 GOL.34: 8 residues within 4Å: Chain C: T.37, C.38, N.39, K.40, F.41, E.167, S.168, C.169 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:N.39, C:N.39, C:N.39, C:K.40, C:F.41, C:F.41, C:E.167, C:S.168 GOL.35: 3 residues within 4Å: Chain A: H.392, P.393 Chain D: W.5 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Water bridges: D:Q.6, D:Q.6 Hydrogen bonds: A:H.392

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Janssen, B.J. et al., Structure of compstatin in complex with complement component C3c reveals a new mechanism of complement inhibition. J.Biol.Chem. (2007)

Release Date

2007-08-14

Peptides

Complement C3: A
Complement C3: B
Complement C3: C
compstatin: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

D
H

Complement C3

Complement C3

Complement C3

compstatin

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