SMTL ID : 4dtf.1

Structure of a VgrG Vibrio cholerae toxin ACD domain in complex with AMP-PNP and Mg++

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

monomer

Ligands

1 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 18 residues within 4Å: Chain A: F.16, F.20, S.24, I.25, G.26, I.27, E.28, E.90, V.92, S.93, P.95, T.176, G.178, R.280, I.333, A.336, L.349 Ligands: MG.4 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:S.24, A:S.24, A:I.27, A:S.93, A:T.176 Water bridges: A:G.26, A:E.28, A:K.45, A:E.90, A:T.176, A:K.272, A:K.272, A:K.272, A:K.272, A:T.337 Salt bridges: A:R.280

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: N.41, Q.44, K.62, N.65, H.87 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.41, A:Q.44, A:K.62 Water bridges: A:D.63, A:N.65

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: E.28, Q.174, E.351, R.353 Ligands: SO4.5 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.351, H2O.12 MG.4: 4 residues within 4Å: Chain A: E.28, E.90, V.92 Ligands: ANP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.28

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 5 residues within 4Å: Chain A: M.64, P.269, K.272, R.353 Ligands: MG.3 7 PLIP interactions: 7 interactions with chain A Water bridges: A:Q.174, A:K.272, A:K.272, A:R.353, A:R.353 Salt bridges: A:K.272, A:R.353 SO4.6: 6 residues within 4Å: Chain A: A.153, G.154, N.155, G.156, I.157, S.158 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.155, A:G.156, A:I.157, A:S.158 Water bridges: A:A.153, A:N.155, A:S.158 SO4.7: 6 residues within 4Å: Chain A: W.113, H.117, I.133, Q.134, S.135, E.136 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.136 Water bridges: A:W.113, A:H.117 Salt bridges: A:H.117 SO4.8: 4 residues within 4Å: Chain A: S.171, Q.174, N.273, R.353 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.273 Water bridges: A:Q.174, A:R.353, A:T.354, A:T.354 Salt bridges: A:R.353

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Durand, E. et al., Structure of a VgrG Vibrio cholerae toxin ACD domain in complex with AMP-PNP and Mg++. J.Biol.Chem. (2012)

Release Date

2012-08-29

Peptides

VgrG protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

VgrG protein

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