SMTL ID : 5lzi.1

Porcine heat-labile enterotoxin R13H in complex with inhibitor MM146

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-pentamer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 2 residues within 4Å: Chain A: A.1 Chain B: R.35 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:A.1, A:A.1, B:R.35, B:R.35 Water bridges: A:A.1 GOL.4: 5 residues within 4Å: Chain B: Y.18, E.46, T.47, P.93, N.94 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.47, B:T.47, B:N.94, B:N.94 Water bridges: B:T.47, B:T.47 GOL.5: 4 residues within 4Å: Chain B: T.4, I.5, T.6, K.84 7 PLIP interactions: 1 interactions with chain C, 6 interactions with chain B Water bridges: C:S.26, B:D.83 Hydrogen bonds: B:T.4, B:I.5, B:T.6, B:T.6, B:T.6 GOL.7: 6 residues within 4Å: Chain C: Y.18, E.46, T.47, F.48, P.93, N.94 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:Y.18, C:Y.18, C:T.47, C:N.94, C:N.94 Water bridges: C:G.45, C:T.47, C:T.47, B:Q.3 GOL.10: 3 residues within 4Å: Chain D: I.58, D.59 Chain E: K.34 6 PLIP interactions: 2 interactions with chain E, 4 interactions with chain D Hydrogen bonds: E:K.34, E:K.34, D:D.59, D:D.59, D:D.59 Water bridges: D:S.60

1 x 7BQ: (2~{R},4~{S},5~{R},6~{R})-5-acetamido-2-[4-[(2~{R})-3-[2-[(2~{S},3~{R},4~{R},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]ethylamino]-3-oxidanylidene-2-(2-phenylethanoylamino)propyl]-1,2,3-triazol-1-yl]-4-oxidanyl-6-[(1~{R},2~{R})-1,2,3-tris(oxidanyl)propyl]oxane-2-carboxylic acid(Non-covalent)

7BQ.2: 15 residues within 4Å: Chain A: E.11, Y.12, H.13, E.51, Q.56, H.57, I.58, Q.61, W.88, N.90, K.91 Chain B: G.33, K.34, R.35 Ligands: PEG.3 18 PLIP interactions: 15 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:E.11, A:Y.12, B:R.35 Hydrogen bonds: A:E.11, A:H.13, A:E.51, A:Q.56, A:Q.61, A:Q.61, A:N.90, A:N.90 Water bridges: A:N.14, A:E.51, A:I.58, A:S.95, B:G.33, B:K.34 Salt bridges: A:H.13

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 1 residues within 4Å: Ligands: 7BQ.2 No protein-ligand interaction detected (PLIP)

4 x 7DB: (2~{R},4~{S},5~{R},6~{R})-5-acetamido-2-[4-[(2~{S})-3-[2-[(2~{S},3~{R},4~{R},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]ethylamino]-3-oxidanylidene-2-(2-phenylethanoylamino)propyl]-1,2,3-triazol-1-yl]-4-oxidanyl-6-[(1~{R},2~{R})-1,2,3-tris(oxidanyl)propyl]oxane-2-carboxylic acid(Non-covalent)

7DB.6: 8 residues within 4Å: Chain B: E.51, Q.56, H.57, I.58, Q.61, W.88, N.90, K.91 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.58 Hydrogen bonds: B:Q.56, B:Q.61, B:Q.61, B:N.90, B:N.90 Water bridges: B:E.51, B:Q.56, B:S.95 7DB.8: 8 residues within 4Å: Chain C: E.51, S.55, Q.56, H.57, Q.61, W.88, N.90, K.91 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:Q.56 Hydrogen bonds: C:E.51, C:Q.56, C:Q.56, C:Q.61, C:Q.61, C:N.90, C:N.90 Water bridges: C:E.51, C:E.51 7DB.11: 15 residues within 4Å: Chain D: E.11, Y.12, H.13, E.51, S.55, Q.56, H.57, I.58, Q.61, W.88, N.90, K.91 Chain E: G.33, K.34, R.35 16 PLIP interactions: 13 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: D:Q.56, E:R.35 Hydrogen bonds: D:E.11, D:H.13, D:E.51, D:Q.56, D:Q.61, D:Q.61, D:N.90, D:N.90 Water bridges: D:E.11, D:H.13, D:E.51, D:E.51, E:G.33, E:G.33 7DB.12: 14 residues within 4Å: Chain A: G.33, K.34, R.35 Chain E: E.11, Y.12, H.13, E.51, Q.56, H.57, I.58, Q.61, W.88, N.90, K.91 15 PLIP interactions: 14 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:E.11, E:H.13, E:E.51, E:Q.56, E:Q.61, E:Q.61, E:N.90, E:N.90 Water bridges: E:E.11, E:H.13, E:N.14, E:E.51, E:E.51, A:G.33 Salt bridges: E:H.13

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.9: 2 residues within 4Å: Chain C: H.13, N.14 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:H.13, C:N.14 Water bridges: C:T.15, C:T.15, C:T.15, C:N.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Heggelund, J.E. et al., Towards new cholera prophylactics and treatment: Crystal structures of bacterial enterotoxins in complex with GM1 mimics. Sci Rep (2017)

Release Date

2017-05-31

Peptides

Heat-labile enterotoxin B chain: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Heat-labile enterotoxin B chain