SMTL ID : 1ez1.1

STRUCTURE OF ESCHERICHIA COLI PURT-ENCODED GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE COMPLEXED WITH MG, AMPPNP, AND GAR

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: S.160, E.279 Ligands: MG.2, ANP.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.279, A:E.279, H2O.2, H2O.4 MG.2: 4 residues within 4Å: Chain A: E.267, E.279 Ligands: MG.1, ANP.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.267, A:E.267, A:E.279, H2O.1 MG.8: 3 residues within 4Å: Chain B: E.84, E.279 Ligands: ANP.12 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.279, H2O.30 MG.9: 3 residues within 4Å: Chain B: E.267, E.279 Ligands: ANP.12 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.267, B:E.267, B:E.279, H2O.35

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 2 residues within 4Å: Chain A: T.2 Chain B: Q.341 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Water bridges: B:N.339, B:Q.341, A:T.2 Hydrogen bonds: A:T.2 ACT.10: 3 residues within 4Å: Chain B: S.240, P.241, L.242 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.242

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 4 residues within 4Å: Chain A: N.100, V.101, P.103, C.104 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.100, A:N.100, A:V.101 Water bridges: A:Y.261 NA.11: 4 residues within 4Å: Chain B: N.100, V.101, P.103, C.104 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:V.101, B:V.101 Water bridges: B:N.100, B:Y.261, B:Y.261

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.5: 21 residues within 4Å: Chain A: R.114, S.130, I.153, K.155, S.160, S.161, G.162, Q.165, E.195, G.196, V.197, V.198, F.200, E.203, Q.225, E.267, F.269, E.279 Ligands: MG.1, MG.2, GAR.6 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:R.114, A:R.114, A:S.130, A:K.155, A:S.161, A:G.162, A:Q.165, A:E.195, A:V.198, A:E.203 Water bridges: A:S.160, A:S.160, A:S.161, A:E.203, A:Q.225, A:Q.225, A:Q.225, A:E.267, A:E.267, A:S.278 Salt bridges: A:R.114, A:K.155 ANP.12: 19 residues within 4Å: Chain B: R.114, S.130, K.155, S.159, S.160, S.161, G.162, Q.165, E.195, V.197, V.198, F.200, E.203, Q.225, E.267, F.269, E.279 Ligands: MG.8, MG.9 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:R.114, B:R.114, B:S.130, B:K.155, B:S.159, B:S.161, B:G.162, B:Q.165, B:E.195, B:V.198, B:E.203, B:E.267 Water bridges: B:E.203, B:H.223, B:Q.225, B:Q.225 Salt bridges: B:R.114, B:K.155

2 x GAR: GLYCINAMIDE RIBONUCLEOTIDE(Non-covalent)

GAR.6: 11 residues within 4Å: Chain A: G.21, E.22, L.23, E.82, I.83, S.161, D.286, K.355, R.362, R.363 Ligands: ANP.5 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:G.21, A:E.22, A:L.23, A:E.82, A:E.82, A:S.161, A:D.286, A:R.363, A:R.363 Water bridges: A:E.22, A:S.161, A:D.286, A:K.355, A:K.355, A:K.355, A:R.362 Salt bridges: A:K.355, A:R.362 GAR.13: 9 residues within 4Å: Chain B: G.21, E.22, L.23, E.82, I.83, D.286, K.355, R.362, R.363 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:G.21, B:E.22, B:L.23, B:E.82, B:E.82, B:D.286, B:R.363, B:R.363 Water bridges: B:Y.44, B:E.82, B:S.161, B:G.228, B:D.229, B:D.286, B:D.286, B:D.286, B:K.355, B:K.355, B:K.355, B:K.355, B:R.362, B:R.362 Salt bridges: B:K.355, B:R.362

1 x MPO: 3[N-MORPHOLINO]PROPANE SULFONIC ACID(Non-covalent)

MPO.7: 7 residues within 4Å: Chain A: D.46, M.50, H.51, R.55, S.56 Chain B: L.8, H.54 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.56, A:S.56 Water bridges: A:D.46, A:A.53, A:H.54 Salt bridges: A:D.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thoden, J.B. et al., Molecular structure of Escherichia coli PurT-encoded glycinamide ribonucleotide transformylase. Biochemistry (2000)

Release Date

2000-08-02

Peptides

PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE 2

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