SMTL ID : 5fob.1

Crystal Structure of Human Complement C3b in complex with Smallpox Inhibitor of Complement (SPICE)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUC.1: 8 residues within 4Å: Chain A: V.21, M.61, G.62, N.63, T.65, K.480, A.481, G.482 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.21, A:N.63, A:A.481 Hydrogen bonds: A:G.62, A:N.63

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.2: 2 residues within 4Å: Chain A: N.178 Chain B: N.191 No protein-ligand interaction detected (PLIP)

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 3 residues within 4Å: Chain A: N.59, Y.467, R.483 Ligand excluded by PLIP CL.30: 2 residues within 4Å: Chain B: I.45, F.46 Ligand excluded by PLIP CL.36: 4 residues within 4Å: Chain B: C.353, G.354, K.357, Q.413 Ligand excluded by PLIP CL.39: 2 residues within 4Å: Chain C: P.69, W.118 Ligand excluded by PLIP CL.40: 2 residues within 4Å: Chain C: L.35, C.36 Ligand excluded by PLIP

24 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 2 residues within 4Å: Chain A: R.268 Chain B: Y.680 Ligand excluded by PLIP GOL.5: 5 residues within 4Å: Chain A: K.405, K.406, Q.407, E.411, Q.414 Ligand excluded by PLIP GOL.6: 5 residues within 4Å: Chain A: E.226, K.227, S.281, R.282, K.283 Ligand excluded by PLIP GOL.7: 3 residues within 4Å: Chain A: M.179, K.203, E.204 Ligand excluded by PLIP GOL.8: 8 residues within 4Å: Chain A: E.211, F.237, L.238, G.240, K.578 Chain B: T.53, E.74, T.76 Ligand excluded by PLIP GOL.9: 5 residues within 4Å: Chain A: G.556, Q.557, Q.558 Chain B: F.46 Chain C: V.84 Ligand excluded by PLIP GOL.10: 6 residues within 4Å: Chain A: I.110, S.197, T.198, N.587, L.589 Ligands: GOL.11 Ligand excluded by PLIP GOL.11: 5 residues within 4Å: Chain A: S.197, T.198, E.199, N.587 Ligands: GOL.10 Ligand excluded by PLIP GOL.12: 7 residues within 4Å: Chain A: F.237, V.243, E.244, L.310, H.311, S.312 Chain B: S.145 Ligand excluded by PLIP GOL.13: 4 residues within 4Å: Chain A: P.270, S.275, G.276, E.277 Ligand excluded by PLIP GOL.18: 4 residues within 4Å: Chain A: K.241 Chain B: Y.106, Q.108, K.143 Ligand excluded by PLIP GOL.19: 10 residues within 4Å: Chain B: I.7, I.8, A.9, E.10, R.115, E.117, Q.135, K.165, A.166, A.167 Ligand excluded by PLIP GOL.20: 5 residues within 4Å: Chain B: Q.404, K.407, I.421, Q.450, M.451 Ligand excluded by PLIP GOL.21: 6 residues within 4Å: Chain B: R.93, T.157, P.185, D.225, T.226, E.227 Ligand excluded by PLIP GOL.22: 3 residues within 4Å: Chain B: F.321, K.323, R.324 Ligand excluded by PLIP GOL.23: 2 residues within 4Å: Chain B: N.808, D.809 Ligand excluded by PLIP GOL.24: 5 residues within 4Å: Chain B: E.390, D.392, M.393, F.427, N.431 Ligand excluded by PLIP GOL.25: 3 residues within 4Å: Chain B: R.251, H.254, Y.514 Ligand excluded by PLIP GOL.26: 5 residues within 4Å: Chain B: K.633, N.634, Q.717, Y.718, N.720 Ligand excluded by PLIP GOL.27: 2 residues within 4Å: Chain B: N.611, R.645 Ligand excluded by PLIP GOL.28: 6 residues within 4Å: Chain B: L.757, R.764, E.767, N.769, P.839, K.841 Ligand excluded by PLIP GOL.29: 4 residues within 4Å: Chain B: H.254, G.515, G.516, G.517 Ligand excluded by PLIP GOL.37: 4 residues within 4Å: Chain C: D.80, G.82, S.89, T.91 Ligand excluded by PLIP GOL.38: 5 residues within 4Å: Chain C: P.9, Y.34, A.50, W.57, L.59 Ligand excluded by PLIP

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

NA.14: 4 residues within 4Å: Chain A: P.505, D.532, V.533, D.535 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.532, A:V.533 NA.31: 4 residues within 4Å: Chain B: D.84, L.85, R.86, K.179 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.84, B:L.85, B:K.179

7 x IOD: IODIDE ION(Non-functional Binders)

IOD.15: 4 residues within 4Å: Chain A: S.16, E.17, N.131, K.133 Ligand excluded by PLIP IOD.16: 2 residues within 4Å: Chain A: R.282, L.286 Ligand excluded by PLIP IOD.17: 5 residues within 4Å: Chain A: D.535, S.536, Q.591, S.592, W.595 Ligand excluded by PLIP IOD.32: 3 residues within 4Å: Chain A: F.40 Chain B: E.284, W.286 Ligand excluded by PLIP IOD.33: 3 residues within 4Å: Chain B: A.9, N.12 Chain C: K.42 Ligand excluded by PLIP IOD.34: 1 residues within 4Å: Chain B: K.391 Ligand excluded by PLIP IOD.35: 3 residues within 4Å: Chain B: K.357, N.415, S.416 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Forneris, F. et al., Regulators of Complement Activity Mediate Inhibitory Mechanisms Through a Common C3B-Binding Mode. Embo J. (2016)

Release Date

2016-04-06

Peptides

COMPLEMENT C3 BETA CHAIN: A
COMPLEMENT C3B ALPHA' CHAIN: B
SMALLPOX INHIBITOR OF COMPLEMENT SPICE, D15L: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

COMPLEMENT C3 BETA CHAIN

COMPLEMENT C3B ALPHA' CHAIN

SMALLPOX INHIBITOR OF COMPLEMENT SPICE, D15L

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