SMTL ID : 1rd9.1

Cholera Toxin B-Pentamer Complexed With Bivalent Nitrophenol-Galactoside Ligand BV2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.44 Å

Oligo State

homo-pentamer

Ligands

5 x BV2: 1,3-BIS-([3-(4-{3-[3-NITRO-5-(GALACTOPYRANOSYLOXY)-BENZOYLAMINO]-PROPYL}-PIPERAZIN-1-YL)-PROPYL-AMINO]-CARBONYLOXY)-2-AMINO-PROPANE(Non-covalent)

BV2.1: 10 residues within 4Å: Chain A: Y.12, E.51, Q.56, H.57, Q.61, W.88, N.90, K.91 Chain B: A.32, G.33 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.61, A:Q.61, A:N.90, A:N.90, A:N.90, A:K.91 Water bridges: A:E.51 BV2.2: 12 residues within 4Å: Chain B: E.11, Y.12, E.51, Q.56, H.57, Q.61, W.88, N.90, K.91 Chain C: A.32, G.33, R.35 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:W.88 Hydrogen bonds: B:Q.56, B:Q.61, B:Q.61, B:N.90, B:N.90, B:N.90, B:K.91 Water bridges: B:E.51 BV2.3: 10 residues within 4Å: Chain C: Y.12, E.51, Q.56, H.57, Q.61, W.88, N.90, K.91 Chain D: A.32, G.33 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:Q.56, C:Q.61, C:Q.61, C:N.90, C:N.90, C:N.90, C:K.91 Water bridges: C:E.51 BV2.4: 10 residues within 4Å: Chain D: Y.12, E.51, Q.56, H.57, Q.61, W.88, N.90, K.91 Chain E: A.32, G.33 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:Q.56, D:Q.61, D:Q.61, D:N.90, D:N.90, D:N.90, D:K.91 Water bridges: D:I.58 BV2.5: 13 residues within 4Å: Chain A: A.32, G.33, K.34, R.35 Chain E: E.11, Y.12, E.51, Q.56, H.57, Q.61, W.88, N.90, K.91 11 PLIP interactions: 9 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: E:W.88, A:K.34 Hydrogen bonds: E:Q.61, E:Q.61, E:N.90, E:N.90, E:N.90, E:K.91 Water bridges: E:I.58, A:K.34 Salt bridges: E:E.11

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.6: 5 residues within 4Å: Chain A: R.35 Chain E: T.1, P.2, D.7, E.11 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A Water bridges: E:Q.3, E:D.7 Hydrogen bonds: A:R.35

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.7: 3 residues within 4Å: Chain A: K.91, T.92 Chain E: T.1 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:T.1, E:T.1, A:T.92

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pickens, J.C. et al., Nonspanning bivalent ligands as improved surface receptor binding inhibitors of the cholera toxin B pentamer. Chem.Biol. (2004)

Release Date

2004-10-26

Peptides

cholera toxin B protein (CTB): ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

D
G

E
H

cholera toxin B protein (CTB)

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