SMTL ID : 7o4w.1

Crystal structure of diphtheria toxin mutant CRM197 with a disulphide bond replaced by a Cys-Acetone-Cys bridge

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

homo-dimer

Ligands

2 x 4Y8: 1-hydroxypropan-2-one(Covalent)

4Y8.1: 4 residues within 4Å: Chain A: A.185, C.186, C.201, N.376 No protein-ligand interaction detected (PLIP) 4Y8.8: 4 residues within 4Å: Chain B: A.185, C.186, C.201, N.376 No protein-ligand interaction detected (PLIP)

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 2 residues within 4Å: Chain A: A.379, S.381 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.381 Water bridges: A:A.379 EDO.3: 9 residues within 4Å: Chain A: P.72, L.73, Q.175, Y.179, N.366, V.370 Chain B: R.455, S.475, P.476 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.175, A:Y.179, A:N.366, A:N.366, B:S.475 EDO.4: 8 residues within 4Å: Chain A: V.452, I.457, P.476, V.477, Y.478, V.483 Chain B: V.370, S.374 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.478, B:S.374 Water bridges: A:R.455 EDO.9: 2 residues within 4Å: Chain B: A.379, S.381 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.381 Water bridges: B:A.379 EDO.10: 9 residues within 4Å: Chain A: R.455, S.475, P.476 Chain B: P.72, L.73, Q.175, Y.179, N.366, V.370 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.475, B:Q.175, B:N.366, B:N.366 EDO.11: 8 residues within 4Å: Chain A: V.370, S.374 Chain B: V.452, I.457, P.476, V.477, Y.478, V.483 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.478, A:S.374 Water bridges: B:R.455

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

PGE.5: 4 residues within 4Å: Chain A: H.21, K.24, I.31 Ligands: PGE.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.24 PGE.6: 8 residues within 4Å: Chain A: Y.20, H.21, G.22, Y.54, Y.65 Chain B: S.446, R.458 Ligands: PGE.5 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.446, B:R.458, A:G.22 PGE.12: 4 residues within 4Å: Chain B: H.21, K.24, I.31 Ligands: PGE.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.24 PGE.13: 8 residues within 4Å: Chain A: S.446, R.458 Chain B: Y.20, H.21, G.22, Y.54, Y.65 Ligands: PGE.12 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.446, A:R.458, B:G.22

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 5 residues within 4Å: Chain A: H.391, K.516, N.524, S.525, K.526 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.526 Water bridges: A:K.516 Salt bridges: A:H.391, A:K.516 ACT.14: 5 residues within 4Å: Chain B: H.391, K.516, N.524, S.525, K.526 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.526 Water bridges: B:K.516 Salt bridges: B:H.391, B:K.516

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carboni, F. et al., Retaining the structural integrity of disulfide bonds in diphtheria toxoid carrier protein is crucial for the effectiveness of glycoconjugate vaccine candidates. Chem Sci (2022)

Release Date

2022-04-06

Peptides

Diphtheria toxin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Diphtheria toxin

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