SMTL ID : 1kj8.1

Crystal Structure of PurT-Encoded Glycinamide Ribonucleotide Transformylase in Complex with Mg-ATP and GAR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: E.278 Ligands: MG.2, ATP.7 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.278, A:E.278, H2O.1, H2O.6 MG.2: 4 residues within 4Å: Chain A: E.266, E.278 Ligands: MG.1, ATP.7 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.266, A:E.266, A:E.278, H2O.1 MG.11: 3 residues within 4Å: Chain B: R.113, E.278 Ligands: ATP.15 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.278, B:E.278, H2O.31 MG.12: 3 residues within 4Å: Chain B: E.266, E.278 Ligands: ATP.15 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.266, B:E.266, B:E.278, H2O.28

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

NA.3: 3 residues within 4Å: Chain A: N.99, V.100, P.102 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.99, A:P.102 Water bridges: A:V.100, A:Y.260, A:Y.260 NA.13: 3 residues within 4Å: Chain B: N.99, V.100, P.102 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.102 Water bridges: B:V.100, B:Y.260, B:Y.260

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 3 residues within 4Å: Chain A: I.82, E.83, S.159 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain A: Q.340 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: R.32 Chain B: R.32 Ligands: EDO.17 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain B: H.215, F.216 Ligand excluded by PLIP

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

ATP.7: 23 residues within 4Å: Chain A: R.113, S.129, I.152, K.154, S.158, S.159, S.160, G.161, Q.164, E.194, G.195, V.196, V.197, F.199, E.202, Q.224, G.227, E.266, F.268, E.278 Ligands: MG.1, MG.2, GAR.8 27 PLIP interactions: 27 interactions with chain A Hydrogen bonds: A:S.129, A:K.154, A:S.158, A:S.160, A:G.161, A:Q.164, A:E.194, A:V.197, A:E.202 Water bridges: A:R.113, A:R.113, A:R.113, A:R.113, A:S.159, A:S.159, A:Q.224, A:Q.224, A:G.227, A:E.266, A:E.266, A:E.266, A:S.277, A:H.284, A:R.362 Salt bridges: A:R.113, A:R.113, A:K.154 ATP.15: 18 residues within 4Å: Chain B: R.113, S.129, K.154, S.158, S.159, S.160, G.161, Q.164, E.194, V.196, V.197, F.199, E.202, E.266, F.268, E.278 Ligands: MG.11, MG.12 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:S.129, B:K.154, B:S.160, B:G.161, B:Q.164, B:E.194, B:V.197, B:E.202 Water bridges: B:R.113, B:Q.224, B:E.266, B:S.277 Salt bridges: B:R.113, B:R.113, B:K.154

2 x GAR: GLYCINAMIDE RIBONUCLEOTIDE(Non-covalent)

GAR.8: 12 residues within 4Å: Chain A: G.20, E.21, L.22, E.81, I.82, S.159, S.160, D.285, K.354, R.361, R.362 Ligands: ATP.7 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:G.20, A:L.22, A:E.81, A:E.81, A:D.285, A:D.285, A:R.362, A:R.362 Water bridges: A:E.21, A:S.159, A:S.159, A:S.159, A:S.160, A:D.285, A:K.354, A:K.354, A:K.354, A:R.361 Salt bridges: A:K.354, A:R.361 GAR.16: 9 residues within 4Å: Chain B: G.20, E.21, L.22, E.81, I.82, D.285, K.354, R.361, R.362 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:G.20, B:L.22, B:E.81, B:E.81, B:D.285, B:R.362, B:R.362 Water bridges: B:D.41, B:Y.43, B:D.228, B:D.285, B:K.354, B:K.354, B:K.354, B:K.354, B:R.361, B:R.361 Salt bridges: B:K.354, B:R.361

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

MPO.9: 7 residues within 4Å: Chain A: D.45, M.49, H.50, R.54, S.55 Chain B: L.7, H.53 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.55 Water bridges: A:S.55 Salt bridges: A:D.45

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

EDO.10: 4 residues within 4Å: Chain A: I.91, R.105, K.108, L.109 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.105 EDO.17: 8 residues within 4Å: Chain A: Q.348 Chain B: E.29, R.32, D.295, L.296, S.297, A.300 Ligands: CL.6 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.32, A:Q.348 Water bridges: B:E.25, B:S.297, A:Q.348, A:R.350 EDO.18: 3 residues within 4Å: Chain B: S.239, P.240, L.241 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.239, B:L.241

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thoden, J.B. et al., PurT-encoded glycinamide ribonucleotide transformylase. Accommodation of adenosine nucleotide analogs within the active site. J.Biol.Chem. (2002)

Release Date

2002-06-28

Peptides

phosphoribosylglycinamide formyltransferase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

phosphoribosylglycinamide formyltransferase 2

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