SMTL ID : 2yb1.1

Structure of an amidohydrolase from Chromobacterium violaceum (EFI target EFI-500202) with bound Mn, AMP and phosphate.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: H.9, D.14, H.39, H.250 Ligands: AMP.4, PO4.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.14, A:D.14, A:H.39, A:H.250 MN.2: 6 residues within 4Å: Chain A: H.7, H.9, E.64, D.248 Ligands: MN.3, PO4.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.7, A:H.9, A:E.64, A:D.248 MN.3: 5 residues within 4Å: Chain A: E.64, H.75, H.191 Ligands: MN.2, PO4.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.64, A:H.75, A:H.191

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.4: 12 residues within 4Å: Chain A: D.14, H.39, H.75, R.99, R.102, S.133, R.134, T.135, F.154, H.250 Ligands: MN.1, PO4.5 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:H.39, A:R.134, A:T.135 Water bridges: A:R.99, A:R.99, A:R.99, A:R.134, A:R.134, A:R.194 Salt bridges: A:R.99, A:R.102, A:R.134 pi-Stacking: A:F.154, A:F.154 pi-Cation interactions: A:R.194

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 13 residues within 4Å: Chain A: H.7, H.9, H.39, E.64, H.75, H.191, R.194, D.248, H.250 Ligands: MN.1, MN.2, MN.3, AMP.4 7 PLIP interactions: 7 interactions with chain A Salt bridges: A:H.7, A:H.9, A:H.39, A:H.75, A:H.191, A:R.194, A:H.250

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cummings, J.A. et al., Prospecting for Unannotated Enzymes: Discovery of a 3',5'-Nucleotide Bisphosphate Phosphatase within the Amidohydrolase Superfamily. Biochemistry (2014)

Release Date

2011-03-16

Peptides

AMIDOHYDROLASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

AMIDOHYDROLASE

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