SMTL ID : 3pkq.2 (2 other biounits)

Q83D Variant of S. Enterica RmlA with dGTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x DGT: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

DGT.1: 16 residues within 4Å: Chain A: L.9, G.11, G.12, S.13, G.14, T.15, R.16, K.26, Q.27, I.55, D.83, S.85, L.109, G.110, D.111 Ligands: MG.2 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:G.11, A:G.12, A:S.13, A:G.14, A:T.15, A:T.15, A:T.15, A:R.16, A:R.16, A:Q.27, A:I.55, A:S.85, A:G.110, A:D.111, A:D.111 Salt bridges: A:R.16, A:K.26, A:K.26, A:K.26, A:D.83 DGT.5: 17 residues within 4Å: Chain B: L.9, G.11, G.12, S.13, G.14, T.15, R.16, K.26, Q.27, I.55, D.83, S.85, L.109, G.110, D.111 Ligands: MG.6, MG.7 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:G.11, B:G.12, B:S.13, B:G.14, B:T.15, B:T.15, B:T.15, B:R.16, B:R.16, B:Q.27, B:I.55, B:G.110, B:D.111, B:D.111 Salt bridges: B:R.16, B:K.26, B:K.26, B:K.26, B:D.83

3 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 4 residues within 4Å: Chain A: K.26, D.111, D.226 Ligands: DGT.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.111, A:D.226 MG.6: 4 residues within 4Å: Chain B: K.26, D.111, D.226 Ligands: DGT.5 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.111, B:D.226 MG.7: 1 residues within 4Å: Ligands: DGT.5 No protein-ligand interaction detected (PLIP)

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 11 residues within 4Å: Chain A: R.4, K.5, D.104, C.105, A.126, V.127, K.129, G.132, F.178, Y.179, D.180 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.5 PEG.4: 8 residues within 4Å: Chain A: Y.32, H.230, L.233, I.234, S.237 Chain B: Y.32, I.234, S.237 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.32, A:H.230, A:S.237, B:S.237

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moretti, R. et al., Expanding the Nucleotide and Sugar 1-Phosphate Promiscuity of Nucleotidyltransferase RmlA via Directed Evolution. J.Biol.Chem. (2011)

Release Date

2011-01-12

Peptides

Glucose-1-phosphate thymidylyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glucose-1-phosphate thymidylyltransferase

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