SMTL ID : 4en9.1

Crystal structure of HA70 (HA3) subcomponent of Clostridium botulinum type C progenitor toxin in complex with alpha 2-6-sialyllactosamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.64 Å

Oligo State

hetero-3-3-mer

Ligands

3 x NAG- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)

NAG-GAL-SIA.1: 11 residues within 4Å: Chain B: N.117, R.257, S.258, D.259, D.310, N.311, H.318, Y.319, Y.320, T.321, R.322 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:R.257, B:N.117, B:R.257, B:R.257, B:S.258, B:D.259, B:R.257, B:D.310, B:N.311, B:Y.319, B:T.321, B:T.321, B:R.322, B:R.322 Water bridges: B:R.257, B:R.257, B:D.259, B:Y.319 Salt bridges: B:R.257 NAG-GAL-SIA.7: 11 residues within 4Å: Chain D: N.117, R.257, S.258, D.259, D.310, N.311, H.318, Y.319, Y.320, T.321, R.322 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:R.257, D:N.117, D:R.257, D:R.257, D:S.258, D:D.259, D:R.257, D:D.310, D:N.311, D:Y.319, D:T.321, D:T.321, D:R.322, D:R.322 Water bridges: D:R.257, D:R.257, D:D.259, D:Y.319 Salt bridges: D:R.257 NAG-GAL-SIA.13: 11 residues within 4Å: Chain F: N.117, R.257, S.258, D.259, D.310, N.311, H.318, Y.319, Y.320, T.321, R.322 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:R.257, F:N.117, F:R.257, F:R.257, F:S.258, F:D.259, F:R.257, F:D.310, F:N.311, F:Y.319, F:T.321, F:T.321, F:R.322, F:R.322 Water bridges: F:R.257, F:R.257, F:D.259, F:Y.319 Salt bridges: F:R.257

15 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.2: 6 residues within 4Å: Chain A: E.123, F.124, S.125 Chain D: S.38, S.40, V.90 Ligand excluded by PLIP MRD.3: 8 residues within 4Å: Chain A: D.79, L.80, G.121, F.122, E.123 Chain B: L.86 Chain D: P.44, L.46 Ligand excluded by PLIP MRD.4: 5 residues within 4Å: Chain A: K.182, F.186 Chain B: I.165, I.166, V.167 Ligand excluded by PLIP MRD.5: 5 residues within 4Å: Chain B: I.61, Y.66, N.114, N.171, S.173 Ligand excluded by PLIP MRD.6: 6 residues within 4Å: Chain A: N.71 Chain B: E.91, P.94, K.97, I.99, D.138 Ligand excluded by PLIP MRD.8: 6 residues within 4Å: Chain C: E.123, F.124, S.125 Chain F: S.38, S.40, V.90 Ligand excluded by PLIP MRD.9: 8 residues within 4Å: Chain C: D.79, L.80, G.121, F.122, E.123 Chain D: L.86 Chain F: P.44, L.46 Ligand excluded by PLIP MRD.10: 5 residues within 4Å: Chain C: K.182, F.186 Chain D: I.165, I.166, V.167 Ligand excluded by PLIP MRD.11: 5 residues within 4Å: Chain D: I.61, Y.66, N.114, N.171, S.173 Ligand excluded by PLIP MRD.12: 6 residues within 4Å: Chain C: N.71 Chain D: E.91, P.94, K.97, I.99, D.138 Ligand excluded by PLIP MRD.14: 6 residues within 4Å: Chain B: S.38, S.40, V.90 Chain E: E.123, F.124, S.125 Ligand excluded by PLIP MRD.15: 8 residues within 4Å: Chain B: P.44, L.46 Chain E: D.79, L.80, G.121, F.122, E.123 Chain F: L.86 Ligand excluded by PLIP MRD.16: 5 residues within 4Å: Chain E: K.182, F.186 Chain F: I.165, I.166, V.167 Ligand excluded by PLIP MRD.17: 5 residues within 4Å: Chain F: I.61, Y.66, N.114, N.171, S.173 Ligand excluded by PLIP MRD.18: 6 residues within 4Å: Chain E: N.71 Chain F: E.91, P.94, K.97, I.99, D.138 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamashita, S. et al., Carbohydrate recognition mechanism of HA70 from Clostridium botulinum deduced from X-ray structures in complexes with sialylated oligosaccharides. Febs Lett. (2012)

Release Date

2012-06-06

Peptides

Hemagglutinin components HA-22/23/53: ACE
Hemagglutinin components HA-22/23/53: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

Hemagglutinin components HA-22/23/53

Hemagglutinin components HA-22/23/53

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