SMTL ID : 1kji.1

Crystal structure of glycinamide ribonucleotide transformylase in complex with Mg-AMPPCP

Coordinates

PDB Format

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, ACP.6 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.278, A:E.278, H2O.5, H2O.6 MG.2: 4 residues within 4Å: Chain A: E.266, E.278 Ligands: MG.1, ACP.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.266, A:E.266, A:E.278, H2O.3 MG.9: 3 residues within 4Å: Chain B: E.278 Ligands: MG.10, ACP.12 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.278, B:E.278, H2O.23, H2O.26 MG.10: 4 residues within 4Å: Chain B: E.266, E.278 Ligands: MG.9, ACP.12 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.266, B:E.266, B:E.278, H2O.29

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

NA.3: 2 residues within 4Å: Chain A: A.52 Chain B: A.52 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.52 NA.4: 4 residues within 4Å: Chain A: E.94, L.98, N.99, V.100 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.94, A:N.99, A:V.100 NA.11: 4 residues within 4Å: Chain B: N.99, V.100, P.102, C.103 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.99, B:V.100, B:P.102 Water bridges: B:E.94, B:Y.260, B:Y.260

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

CL.5: 3 residues within 4Å: Chain A: R.118, R.132, F.133 Ligand excluded by PLIP

2 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.6: 21 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, E.266, F.268, E.278 Ligands: MG.1, MG.2 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:R.113, A:R.113, A:S.129, A:K.154, A:S.160, A:G.161, A:Q.164, A:E.194, A:V.197, A:E.202 Water bridges: A:E.83, A:Q.224, A:E.266, A:E.266, A:E.266, A:E.278, A:E.278, A:H.284 Salt bridges: A:R.113, A:K.154 ACP.12: 19 residues within 4Å: Chain B: R.113, S.129, K.154, S.158, S.159, S.160, G.161, Q.164, E.194, G.195, V.197, F.199, E.202, Q.224, E.266, F.268, E.278 Ligands: MG.9, MG.10 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:R.113, B:R.113, B:S.129, B:K.154, B:S.160, B:G.161, B:Q.164, B:E.194, B:V.197, B:E.202, B:E.278 Water bridges: B:E.83, B:E.266, B:E.266, B:E.278, B:E.278 Salt bridges: B:R.113, B:K.154

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

MPO.7: 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:D.45 Salt bridges: A:D.45

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

EDO.8: 3 residues within 4Å: Chain A: N.59, D.62, R.68 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.59, A:D.62, A:R.68 Water bridges: A:R.42

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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