SMTL ID : 5lzh.1

Cholera toxin classical B-pentamer in complex with inhibitor PC262

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.13 Å

Oligo State

homo-pentamer

Ligands

5 x 7BN: (2~{R},4~{S},5~{R},6~{R})-5-acetamido-2-[4-[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-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)

7BN.1: 14 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 13 PLIP interactions: 2 interactions with chain B, 11 interactions with chain A Water bridges: B:G.33, B:G.33, A:E.51, A:Q.56 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 Salt bridges: A:H.13 7BN.2: 15 residues within 4Å: Chain B: E.11, Y.12, H.13, E.51, Q.56, H.57, I.58, Q.61, W.88, N.90, K.91 Chain C: G.33, K.34, R.35 Ligands: MRD.3 13 PLIP interactions: 2 interactions with chain C, 11 interactions with chain B Water bridges: C:G.33, C:G.33, B:N.14, B:I.58 Hydrogen bonds: B:E.11, B:H.13, B:E.51, B:Q.56, B:Q.61, B:Q.61, B:N.90, B:N.90 Salt bridges: B:H.13 7BN.4: 14 residues within 4Å: Chain C: E.11, Y.12, H.13, E.51, Q.56, H.57, I.58, Q.61, W.88, N.90, K.91 Chain D: G.33, K.34, R.35 12 PLIP interactions: 10 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:E.11, C:H.13, C:E.51, C:Q.56, C:Q.61, C:Q.61, C:N.90, C:N.90 Water bridges: C:E.51, D:G.33, D:R.35 Salt bridges: C:H.13 7BN.7: 14 residues within 4Å: Chain D: E.11, Y.12, H.13, E.51, Q.56, H.57, I.58, Q.61, W.88, N.90, K.91 Chain E: G.33, K.34, R.35 15 PLIP interactions: 12 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: D:E.11, 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:Q.56, D:I.58, E:G.33, E:G.33 Salt bridges: D:H.13 7BN.9: 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 14 PLIP interactions: 2 interactions with chain A, 12 interactions with chain E Hydrophobic interactions: A:R.35 Water bridges: A:G.33, E:Q.56, E:Q.56 Hydrogen bonds: E:E.11, E:H.13, E:E.51, E:Q.56, E:Q.61, E:Q.61, E:Q.61, E:N.90, E:N.90 Salt bridges: E:H.13

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

MRD.3: 3 residues within 4Å: Chain B: E.11, H.13 Ligands: 7BN.2 1 PLIP interactions: 1 interactions with chain B Water bridges: B:H.13

3 x CA: CALCIUM ION(Non-covalent)

CA.5: 2 residues within 4Å: Chain C: E.79 Ligands: CA.6 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.79, C:E.79 CA.6: 2 residues within 4Å: Chain C: E.79 Ligands: CA.5 No protein-ligand interaction detected (PLIP) CA.11: 1 residues within 4Å: Chain E: E.79 No protein-ligand interaction detected (PLIP)

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

TRS.8: 6 residues within 4Å: Chain D: T.78, A.80, N.103 Chain E: Y.76, L.77, E.79 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:Y.76, D:T.78, D:N.103, D:N.103

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

PEG.10: 6 residues within 4Å: Chain E: F.25, T.41, F.42, K.43, G.45, T.47 No protein-ligand interaction detected (PLIP)

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

Cholera enterotoxin B subunit: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Cholera enterotoxin B subunit

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