SMTL ID : 1rf2.1

Cholera Toxin B-Pentamer Complexed With Bivalent Nitrophenol-Galactoside Ligand BV4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-pentamer

Ligands

5 x BV4: 1,3-BIS-([3-[3-[3-(4-{3-[3-NITRO-5-(GALACTOPYRANOSYLOXY)-BENZOYLAMINO]-PROPYL}-PIPERAZIN-1-YL)-PROPYLAMINO-3,4-DIOXO-CYCLOBUTENYL]-AMINO-PROPOXY-ETHOXY-ETHOXY]-PROPYL-]AMINO-CARBONYLOXY)-2-AMINO-PROPANE(Non-covalent)

BV4.1: 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 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.88 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, B:G.33 BV4.2: 10 residues within 4Å: Chain B: Y.12, E.51, Q.56, H.57, Q.61, W.88, N.90, K.91 Chain C: A.32, G.33 10 PLIP interactions: 10 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:I.58, B:K.91 BV4.3: 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 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:W.88 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, C:I.58 BV4.4: 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 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:W.88 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:E.51 BV4.5: 10 residues within 4Å: Chain A: A.32, G.33 Chain E: Y.12, E.51, Q.56, H.57, Q.61, W.88, N.90, K.91 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:E.51, E:Q.61, E:Q.61, E:N.90, E:N.90, E:N.90 Water bridges: E:N.14

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 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain E Hydrogen bonds: A:R.35, E:T.1 Water bridges: E:Q.3, E:D.7

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

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