SMTL ID : 2nt8.1

ATP bound at the active site of a PduO type ATP:co(I)rrinoid adenosyltransferase from Lactobacillus reuteri

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

homo-trimer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: K.58 Chain B: N.191 Ligands: ATP.3 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain B: K.58 Chain C: N.191 Ligands: ATP.8 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain A: N.191 Chain C: K.58 Ligands: ATP.13 No protein-ligand interaction detected (PLIP)

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 17 residues within 4Å: Chain A: E.71, W.75, V.161, I.165, R.168 Chain B: E.71, W.75, V.161, I.165, R.168 Chain C: E.71, W.75, V.161, I.165, R.168 Ligands: SO4.7, SO4.12 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: B:E.71, B:R.168, A:E.71, A:R.168, C:R.168 SO4.7: 17 residues within 4Å: Chain A: E.71, W.75, V.161, I.165, R.168 Chain B: E.71, W.75, V.161, I.165, R.168 Chain C: E.71, W.75, V.161, I.165, R.168 Ligands: SO4.2, SO4.12 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: B:E.71, B:R.168, A:E.71, A:R.168, C:R.168 SO4.12: 17 residues within 4Å: Chain A: E.71, W.75, V.161, I.165, R.168 Chain B: E.71, W.75, V.161, I.165, R.168 Chain C: E.71, W.75, V.161, I.165, R.168 Ligands: SO4.2, SO4.7 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: B:E.71, B:R.168, A:E.71, A:R.168, C:R.168

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

ATP.3: 19 residues within 4Å: Chain A: Y.39, T.40, K.41, N.42, G.43, Q.47, T.48, R.49, K.58, V.63, Y.66, G.67 Chain B: R.167, E.170, R.171, N.191, D.195 Ligands: MG.1, GOL.4 24 PLIP interactions: 13 interactions with chain A, 11 interactions with chain B Hydrogen bonds: A:T.40, A:K.41, A:G.43, A:Q.47, A:T.48, A:R.49, B:R.167, B:R.167, B:R.167, B:E.170, B:R.171, B:N.191 Water bridges: A:R.49, A:R.49, A:K.58, A:K.58, A:Y.66, B:N.191, B:R.192 Salt bridges: A:K.58, A:K.58, B:R.167 pi-Cation interactions: B:R.167, B:R.167 ATP.8: 19 residues within 4Å: Chain B: Y.39, T.40, K.41, N.42, G.43, Q.47, T.48, R.49, K.58, V.63, Y.66, G.67 Chain C: R.167, E.170, R.171, N.191, D.195 Ligands: MG.6, GOL.9 24 PLIP interactions: 13 interactions with chain B, 11 interactions with chain C Hydrogen bonds: B:T.40, B:K.41, B:G.43, B:Q.47, B:T.48, B:R.49, C:R.167, C:R.167, C:R.167, C:E.170, C:R.171, C:N.191 Water bridges: B:T.40, B:R.49, B:R.49, B:K.58, B:K.58, C:N.191, C:R.192 Salt bridges: B:K.58, B:K.58, C:R.167 pi-Cation interactions: C:R.167, C:R.167 ATP.13: 19 residues within 4Å: Chain A: R.167, E.170, R.171, N.191, D.195 Chain C: Y.39, T.40, K.41, N.42, G.43, Q.47, T.48, R.49, K.58, V.63, Y.66, G.67 Ligands: MG.11, GOL.14 23 PLIP interactions: 13 interactions with chain C, 10 interactions with chain A Hydrogen bonds: C:T.40, C:K.41, C:G.43, C:Q.47, C:T.48, C:R.49, A:R.167, A:R.167, A:R.167, A:R.171, A:N.191 Water bridges: C:R.49, C:R.49, C:K.58, C:K.58, C:Y.66, A:N.191, A:R.192 Salt bridges: C:K.58, C:K.58, A:R.167 pi-Cation interactions: A:R.167, A:R.167

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: N.42, G.43, Q.47, T.48, R.49, I.55 Ligands: ATP.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.42, A:T.48, A:R.49 GOL.5: 4 residues within 4Å: Chain A: L.56, R.62, P.111, E.180 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.62 Water bridges: A:D.60, A:D.60, A:A.112, A:Q.181 GOL.9: 7 residues within 4Å: Chain B: N.42, G.43, Q.47, T.48, R.49, I.55 Ligands: ATP.8 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.42, B:T.48, B:R.49 Water bridges: B:T.40 GOL.10: 4 residues within 4Å: Chain B: L.56, R.62, P.111, E.180 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.62 Water bridges: B:D.60, B:A.112, B:E.180, B:Q.181 GOL.14: 7 residues within 4Å: Chain C: N.42, G.43, Q.47, T.48, R.49, I.55 Ligands: ATP.13 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.42, C:R.49 GOL.15: 4 residues within 4Å: Chain C: L.56, R.62, P.111, E.180 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.62 Water bridges: C:D.60, C:D.60, C:A.112, C:Q.181

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

St Maurice, M. et al., Structural characterization of the active site of the PduO-type ATP:Co(I)rrinoid adenosyltransferase from Lactobacillus reuteri. J.Biol.Chem. (2007)

Release Date

2006-11-21

Peptides

Cobalamin adenosyltransferase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Cobalamin adenosyltransferase