SMTL ID : 4hut.1

Structure of ATP:co(I)rrinoid adenosyltransferase (CobA) from Salmonella enterica in complex with four and five-coordinate cob(II)alamin and ATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: T.37, E.123 Ligands: ATP.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.37, A:E.123, H2O.1, H2O.1 MG.6: 4 residues within 4Å: Chain B: T.37, K.61, E.123 Ligands: ATP.7 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.37, B:E.123, H2O.8, H2O.8

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

ATP.2: 15 residues within 4Å: Chain A: N.32, G.33, K.34, G.35, K.36, T.37, T.38, E.123, R.156, H.177, F.179, D.190 Chain B: R.46 Ligands: MG.1, B12.3 20 PLIP interactions: 19 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.32, A:K.34, A:K.34, A:G.35, A:K.36, A:T.37, A:T.38, A:T.38, A:R.156, A:D.190 Water bridges: A:K.36, A:K.36, A:T.37, A:T.37, A:T.38 Salt bridges: A:K.34, A:K.36, A:K.36, B:R.46 pi-Stacking: A:H.177 ATP.7: 15 residues within 4Å: Chain A: R.46 Chain B: N.32, G.33, K.34, G.35, K.36, T.37, T.38, E.123, R.156, H.177, F.179, D.190 Ligands: MG.6, B12.8 20 PLIP interactions: 19 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.32, B:K.34, B:K.34, B:G.35, B:K.36, B:T.37, B:T.37, B:T.38, B:T.38, B:R.156 Water bridges: B:K.34, B:K.36, B:K.36, B:T.38, B:Y.126 Salt bridges: B:K.34, B:K.36, B:K.36, A:R.46 pi-Stacking: B:H.177

2 x B12: COBALAMIN(Non-covalent)

B12.3: 14 residues within 4Å: Chain A: I.60, K.61, T.63, W.64, W.88, E.123, Y.126, Y.130, R.156, F.179, A.185, D.190, Y.191 Ligands: ATP.2 17 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: A:I.60, A:W.64, A:W.64, A:W.64, A:Y.126, A:F.179 Hydrogen bonds: A:W.64, A:Y.130, A:R.156, A:A.185, A:D.190 Water bridges: A:R.156, A:F.179, A:V.183, A:D.190, B:R.46 Metal complexes: B12.3 B12.8: 22 residues within 4Å: Chain A: V.12, R.15, V.16, R.46 Chain B: I.60, K.61, G.62, T.63, W.64, G.85, F.86, T.87, W.88, E.123, Y.126, Y.130, R.156, F.179, A.185, D.190, Y.191 Ligands: ATP.7 30 PLIP interactions: 7 interactions with chain A, 23 interactions with chain B, Hydrophobic interactions: A:V.12, A:V.16, B:I.60, B:I.60, B:W.64, B:W.64, B:W.88, B:W.88, B:W.88, B:E.123, B:F.179, B:Y.191 Hydrogen bonds: A:R.15, B:K.61, B:G.62, B:T.63, B:T.63, B:W.64, B:F.86, B:T.87, B:T.87, B:A.185, B:D.190 Water bridges: A:R.15, A:R.46, A:R.46, A:R.46, B:Y.130, B:R.156, B:Y.191

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

EDO.4: 4 residues within 4Å: Chain A: L.142, N.143, R.145, P.146 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.145, A:P.146 Water bridges: A:L.142, A:N.143, A:R.145 EDO.5: 3 residues within 4Å: Chain A: V.48, G.49 Chain B: N.70 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:L.71, A:G.51, A:H.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moore, T.C. et al., Structural Insights into the Mechanism of Four-Coordinate Cob(II)alamin Formation in the Active Site of the Salmonella enterica ATP:Co(I)rrinoid Adenosyltransferase Enzyme: Critical Role of Residues Phe91 and Trp93. Biochemistry (2012)

Release Date

2013-01-23

Peptides

Cob(I)yrinic acid a,c-diamide adenosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cob(I)yrinic acid a,c-diamide adenosyltransferase