SMTL ID : 3vez.1

Crystal structure of the O-carbamoyltransferase TobZ K443A variant in complex with ATP, ADP and carbamoyl phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x FE2: FE (II) ION(Non-covalent)

FE2.1: 5 residues within 4Å: Chain A: H.120, H.124, D.143, D.344 Ligands: ADP.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.120, A:H.124, A:D.143, A:D.344

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: S.536, N.538 Ligands: ATP.4, CP.5 5 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions, 3 Ligand-Water interactions Metal complexes: A:S.536, CP.5, H2O.6, H2O.11, H2O.11

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

ADP.3: 21 residues within 4Å: Chain A: H.20, W.77, H.120, H.124, D.143, G.144, Q.145, G.174, F.175, Y.177, E.178, P.191, G.192, L.291, G.316, V.317, L.319, N.320, S.343, D.344 Ligands: FE2.1 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:G.144, A:Q.145, A:Q.145, A:E.178, A:E.178, A:G.316, A:N.320, A:D.344, A:D.344 Water bridges: A:G.192, A:G.192 Salt bridges: A:H.20, A:H.20, A:H.120, A:H.124

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

ATP.4: 17 residues within 4Å: Chain A: K.45, G.192, M.195, G.196, T.322, R.424, R.455, P.456, T.482, H.498, S.502, T.503, R.504, N.538, R.540 Ligands: MG.2, CP.5 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:G.192, A:G.196, A:R.455, A:S.502, A:S.502, A:R.504, A:N.538 Water bridges: A:R.424, A:R.424, A:R.424, A:R.451, A:R.504 Salt bridges: A:K.45, A:K.45, A:R.424, A:R.424, A:R.455, A:R.455 pi-Stacking: A:H.498

1 x CP: PHOSPHORIC ACID MONO(FORMAMIDE)ESTER(Non-covalent)

CP.5: 10 residues within 4Å: Chain A: R.424, A.425, R.451, M.479, R.504, N.534, T.535, S.536 Ligands: MG.2, ATP.4 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:A.425, A:R.504, A:N.534, A:T.535, A:S.536 Water bridges: A:R.424, A:R.424, A:R.451 Salt bridges: A:R.424, A:R.451, A:R.504

1 x K: POTASSIUM ION(Non-covalent)

K.6: 4 residues within 4Å: Chain A: L.328, T.329, R.330, V.333 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Parthier, C. et al., The O-Carbamoyltransferase TobZ Catalyzes an Ancient Enzymatic Reaction. Angew.Chem.Int.Ed.Engl. (2012)

Release Date

2012-01-25

Peptides

O-carbamoyltransferase TobZ: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

O-carbamoyltransferase TobZ