SMTL ID : 4e1d.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

monomer

Ligands

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 18 residues within 4Å: Chain A: F.16, P.17, F.20, S.24, I.25, G.26, I.27, E.28, V.92, S.93, P.95, T.176, R.280, I.333, A.336, L.349 Ligands: MN.2, MN.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:P.17, A:S.24, A:I.27, A:S.93, A:T.176 Water bridges: A:G.26, A:E.28, A:E.90, A:E.90 Salt bridges: A:R.280 pi-Stacking: A:F.16

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

MN.2: 5 residues within 4Å: Chain A: E.28, Q.174, E.351 Ligands: ADP.1, MN.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.28, A:E.28, A:E.351 MN.3: 4 residues within 4Å: Chain A: E.28, E.90 Ligands: ADP.1, MN.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.28, A:E.90, H2O.6

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

SO4.4: 3 residues within 4Å: Chain A: P.269, K.272, R.353 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.272, A:R.353 SO4.5: 6 residues within 4Å: Chain A: A.153, G.154, N.155, G.156, I.157, S.158 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.155, A:N.155, A:G.156, A:I.157, A:S.158 SO4.6: 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:W.113 Salt bridges: A:H.117

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Durand, E. et al., Structure and functional characterization of the Vibrio cholerae toxin from the VgrG/MARTX family. 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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