SMTL ID : 3ves.1

Crystal structure of the O-carbamoyltransferase TobZ in complex with AMPCPP and carbamoyl phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.23 Å

Oligo State

monomer

Ligands

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

CP.1: 11 residues within 4Å: Chain A: R.424, A.425, K.449, R.451, M.479, R.504, N.534, T.535, S.536 Ligands: APC.2, MN.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:A.425, A:A.425, A:R.504, A:S.536 Water bridges: A:R.424, A:R.424, A:R.451 Salt bridges: A:R.424, A:K.449, A:R.451, A:R.504

1 x APC: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER(Non-covalent)

APC.2: 21 residues within 4Å: Chain A: G.192, K.193, M.195, G.196, T.322, R.424, K.449, R.451, R.455, P.456, T.482, H.498, S.502, T.503, R.504, S.536, N.538, R.540, G.541 Ligands: CP.1, MN.3 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:G.192, A:G.192, A:G.196, A:R.424, A:R.451, A:R.455, A:R.455, A:S.502, A:S.502, A:R.504, A:N.538, A:G.541 Water bridges: A:P.423, A:P.423, A:R.424, A:R.424, A:R.451, A:T.503, A:S.536 Salt bridges: A:K.449, A:R.451, A:R.455 pi-Stacking: A:H.498

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

MN.3: 3 residues within 4Å: Chain A: S.536 Ligands: CP.1, APC.2 4 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:S.536, H2O.1, H2O.1, CP.1

1 x K: POTASSIUM ION(Non-covalent)

K.4: 2 residues within 4Å: Chain A: L.328, V.333 No protein-ligand interaction detected (PLIP)

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

FE2.5: 4 residues within 4Å: Chain A: H.120, H.124, D.143, D.344 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.120, A:H.124, A:D.143, A:D.344, H2O.5

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 8 residues within 4Å: Chain A: E.375, F.376, V.381, A.415, Q.416, G.417, R.429, G.566 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:F.376, A:G.417, A:G.417, A:R.429, A:G.566 Water bridges: A:F.376

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

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