SMTL ID : 4dtl.1

Structure of a VgrG Vibrio cholerae toxin ACD domain in complex with ATP and Mn++

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

monomer

Ligands

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 22 residues within 4Å: Chain A: F.16, S.24, G.26, I.27, E.28, D.63, E.90, V.92, S.93, P.95, Q.174, T.176, G.178, K.272, I.333, A.336, L.349, E.351, R.353 Ligands: MN.3, MN.4, SO4.5 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.24, A:S.24, A:I.27, A:S.93, A:T.176, A:R.353 Water bridges: A:G.26, A:Q.174, A:K.272, A:K.272, A:T.337 Salt bridges: A:K.272 pi-Stacking: A:F.16

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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.41, A:Q.44, A:K.62

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 5 residues within 4Å: Chain A: E.28, Q.174, E.351 Ligands: ATP.1, MN.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.28, A:E.28, A:E.351 MN.4: 4 residues within 4Å: Chain A: E.28, E.90 Ligands: ATP.1, MN.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.28, A:E.90

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

SO4.5: 4 residues within 4Å: Chain A: P.269, K.272, R.353 Ligands: ATP.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.174 Water bridges: A:K.272 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.136 Water bridges: A:D.137 Salt bridges: A:H.117

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 ATP and Mn++. 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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