SMTL ID : 4bol.1

Crystal structure of AmpDh2 from Pseudomonas aeruginosa in complex with pentapeptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x J0J: D-ALANYL-N-[(2S,6R)-6-AMINO-6-CARBOXY-1-{[(1R)-1-CARBOXYETHYL]AMINO}-1-OXOHEXAN-2-YL]-D-GLUTAMINE(Non-covalent)

J0J.1: 20 residues within 4Å: Chain A: H.42, Y.43, L.55, G.59, V.60, S.61, A.62, R.83, W.85, H.86, A.87, G.88, W.97, N.99, E.106, H.153, R.160, K.161 Chain B: R.95 Ligands: ZN.2 17 PLIP interactions: 14 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:H.86 Hydrogen bonds: A:H.86, A:A.87, A:G.88, A:N.99, A:E.106 Water bridges: A:R.83, A:R.83, A:N.99, A:K.161, B:R.149, B:R.149 Salt bridges: A:R.83, A:H.153, A:R.160, A:K.161, B:R.95 J0J.4: 19 residues within 4Å: Chain A: R.95 Chain B: H.42, L.55, G.59, V.60, S.61, A.62, R.83, W.85, H.86, A.87, G.88, W.97, N.99, E.106, H.153, R.160, K.161 Ligands: ZN.3 21 PLIP interactions: 19 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.55, B:V.60, B:V.60, B:W.85, B:H.86, B:W.97 Hydrogen bonds: B:H.86, B:A.87, B:G.88, B:N.99, B:E.106 Water bridges: B:R.83, B:R.83, B:R.83, B:N.99, A:R.95 Salt bridges: B:R.83, B:H.153, B:R.160, B:K.161, A:R.95

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.42, H.153, K.161, D.163 Ligands: J0J.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.42, A:H.153, A:D.163, H2O.25 ZN.3: 5 residues within 4Å: Chain B: H.42, H.153, K.161, D.163 Ligands: J0J.4 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.42, B:H.153, B:D.163, B:D.163, H2O.261

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Martinez-Caballero, S. et al., Reaction Products and the X-Ray Structure of Ampdh2, a Virulence Determinant of Pseudomonas Aeruginosa. J.Am.Chem.Soc. (2013)

Release Date

2013-07-17

Peptides

AMPDH2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

AMPDH2