SMTL ID : 7lvb.1 (1 other biounit)

CHOLERA TOXIN B SUBUNIT WITH ATTACHED SIV EPITOPE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-pentamer

Ligands

5 x GAL: beta-D-galactopyranose(Non-covalent)

GAL.1: 7 residues within 4Å: Chain A: E.51, Q.56, H.57, Q.61, W.88, N.90, K.91 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.61, A:Q.61, A:N.90, A:N.90, A:K.91 Water bridges: A:I.58, A:K.91 Salt bridges: A:K.91 GAL.5: 7 residues within 4Å: Chain B: E.51, Q.56, H.57, Q.61, W.88, N.90, K.91 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Q.56, B:Q.61, B:Q.61, B:N.90, B:N.90, B:K.91 Water bridges: B:E.51 Salt bridges: B:K.91 GAL.8: 7 residues within 4Å: Chain C: E.51, Q.56, H.57, Q.61, W.88, N.90, K.91 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:Q.56, C:Q.61, C:Q.61, C:N.90, C:N.90, C:K.91 Water bridges: C:E.51, C:K.91 Salt bridges: C:K.91 GAL.11: 7 residues within 4Å: Chain D: E.51, Q.56, H.57, Q.61, W.88, N.90, K.91 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:Q.61, D:Q.61, D:N.90, D:N.90, D:K.91 Water bridges: D:I.58, D:K.91 Salt bridges: D:K.91 GAL.15: 7 residues within 4Å: Chain E: E.51, Q.56, H.57, Q.61, W.88, N.90, K.91 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:Q.61, E:Q.61, E:N.90, E:N.90, E:K.91 Water bridges: E:K.91

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

PGE.2: 4 residues within 4Å: Chain A: E.11, Y.12 Chain B: R.35 Ligands: CL.4 No protein-ligand interaction detected (PLIP) PGE.3: 4 residues within 4Å: Chain A: R.35 Chain E: E.11, Y.12 Ligands: CL.16 No protein-ligand interaction detected (PLIP) PGE.6: 4 residues within 4Å: Chain B: E.11, Y.12 Chain C: R.35 Ligands: CL.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.11 PGE.9: 4 residues within 4Å: Chain C: E.11, Y.12 Chain D: K.34, R.35 1 PLIP interactions: 1 interactions with chain C Water bridges: C:H.13 PGE.10: 5 residues within 4Å: Chain B: T.78, E.79 Chain C: Y.76, L.77, E.79 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:E.79, C:E.79 Water bridges: B:K.81, C:E.79 PGE.12: 4 residues within 4Å: Chain D: E.11, Y.12 Chain E: R.35 Ligands: CL.13 No protein-ligand interaction detected (PLIP)

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 3 residues within 4Å: Chain A: Y.12, H.13 Ligands: PGE.2 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain B: Y.12, H.13 Ligands: PGE.6 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain D: Y.12, H.13 Ligands: PGE.12 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain D: K.91, T.92 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain E: H.13 Ligands: PGE.3 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rahman, M.A. et al., Cholera toxin B scaffolded, focused SIV V2 epitope elicits antibodies that influence the risk of SIV mac251 acquisition in macaques. Front Immunol (2023)

Release Date

2022-03-02

Peptides

Cholera enterotoxin B-subunit,Surface protein gp120: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

D
G

E
H

Cholera enterotoxin B-subunit,Surface protein gp120

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