SMTL ID : 7lvb.2 (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:E.51, A:Q.56, A:Q.61, A:Q.61, A:N.90, A:N.90 Water bridges: A:I.58 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 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Q.61, B:Q.61, B:N.90, B:N.90, B:K.91 Water bridges: B:E.51, B:I.58, B:K.91 Salt bridges: B:K.91 GAL.10: 7 residues within 4Å: Chain C: E.51, Q.56, H.57, Q.61, W.88, N.90, K.91 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Q.56, C:Q.61, C:Q.61, C:N.90, C:N.90, C:K.91 Salt bridges: C:K.91 GAL.14: 7 residues within 4Å: Chain D: E.51, Q.56, H.57, Q.61, W.88, N.90, K.91 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:Q.61, D:Q.61, D:N.90, D:N.90, D:K.91 Water bridges: D:E.51 Salt bridges: D:K.91 GAL.18: 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 Salt bridges: E:K.91

9 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: 6 residues within 4Å: Chain A: T.78, E.79, A.80 Chain B: Y.76, L.77, E.79 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:E.79 Hydrogen bonds: A:E.79 PGE.6: 5 residues within 4Å: Chain B: E.11, Y.12 Chain C: K.34, R.35 Ligands: CL.8 No protein-ligand interaction detected (PLIP) PGE.7: 4 residues within 4Å: Chain B: F.25, F.42, K.43, G.45 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.41 PGE.11: 4 residues within 4Å: Chain C: E.11, Y.12 Chain D: R.35 Ligands: CL.13 No protein-ligand interaction detected (PLIP) PGE.12: 6 residues within 4Å: Chain C: T.78, E.79, A.80 Chain D: Y.76, L.77, E.79 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:Y.76 Water bridges: C:K.81 PGE.15: 5 residues within 4Å: Chain D: E.11, Y.12 Chain E: K.34, R.35 Ligands: CL.17 No protein-ligand interaction detected (PLIP) PGE.16: 4 residues within 4Å: Chain D: F.25, F.42, K.43, G.45 No protein-ligand interaction detected (PLIP) PGE.19: 5 residues within 4Å: Chain A: K.34, R.35 Chain E: E.11, Y.12 Ligands: CL.20 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.11

6 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.8: 3 residues within 4Å: Chain B: Y.12, H.13 Ligands: PGE.6 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain B: H.18, T.19 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain C: Y.12, H.13 Ligands: PGE.11 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain D: Y.12, H.13 Ligands: PGE.15 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain E: H.13 Ligands: PGE.19 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
A

B
B

C
C

D
I

E
J

Cholera enterotoxin B-subunit,Surface protein gp120

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