SMTL ID : 3vet.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

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

ADP.1: 19 residues within 4Å: Chain A: G.192, M.195, G.196, T.322, R.424, K.449, R.451, R.455, P.456, H.498, S.502, T.503, R.504, S.536, N.538, R.540, G.541 Ligands: CP.2, MN.5 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:R.451, A:R.455, A:S.502, A:S.502, A:R.504, A:N.538, A:G.541 Water bridges: A:G.192, A:R.424, A:R.424, A:R.424, A:R.504, A:R.540 Salt bridges: A:R.424, A:K.449, A:R.451, A:R.455, A:R.455, A:R.540, A:R.540 pi-Cation interactions: A:H.498 ADP.3: 22 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, M.195, L.291, G.316, V.317, L.319, N.320, S.343, D.344 Ligands: TOY.4, FE2.7 16 PLIP interactions: 16 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:H.20, A:G.192, A:G.192 Salt bridges: A:H.20, A:H.20, A:H.120, A:H.124

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

CP.2: 10 residues within 4Å: Chain A: R.424, A.425, K.449, M.479, R.504, N.534, T.535, S.536 Ligands: ADP.1, MN.5 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:A.425, A:A.425, A:R.451, A:R.504, A:S.536 Water bridges: A:R.424, A:R.424 Salt bridges: A:R.424, A:K.449, A:R.504

1 x TOY: TOBRAMYCIN(Non-covalent)

TOY.4: 10 residues within 4Å: Chain A: D.18, H.20, Y.48, F.175, E.178, E.182, D.189, D.234, Y.236 Ligands: ADP.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:E.182, A:D.234, A:D.234 Water bridges: A:H.20, A:Y.48, A:Y.48, A:Q.145, A:G.188, A:G.188, A:D.234 Salt bridges: A:H.20

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

MN.5: 3 residues within 4Å: Chain A: S.536 Ligands: ADP.1, CP.2 4 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: A:S.536, CP.2, H2O.12, H2O.12

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)

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

FE2.7: 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 EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 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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