SMTL ID : 2cnq.1

Atomic resolution structure of SAICAR-synthase from Saccharomyces cerevisiae complexed with ADP, AICAR, succinate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.00 Å

Oligo State

monomer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 17 residues within 4Å: Chain A: G.18, K.19, V.20, R.21, I.23, L.31, F.33, H.75, H.110, K.111, H.112, L.114, K.164, E.219, V.232, D.233 Ligands: MG.8 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:K.19, A:V.20, A:R.21, A:H.75, A:H.112, A:K.164, A:E.219, A:D.233 Water bridges: A:K.19, A:K.19, A:K.19, A:K.19, A:R.21, A:A.165, A:K.217, A:K.217, A:K.217, A:K.217, A:E.219 Salt bridges: A:K.19, A:R.21 ADP.5: 10 residues within 4Å: Chain A: K.19, S.40, A.41, Y.42, D.43, H.170, D.171, K.260, R.264 Ligands: AMZ.2 27 PLIP interactions: 27 interactions with chain A Hydrogen bonds: A:S.40, A:Y.42, A:D.43, A:D.43, A:D.43, A:D.171, A:D.171 Water bridges: A:Y.42, A:H.170, A:D.171, A:K.260, A:K.260, A:K.260, A:K.260, A:K.260, A:K.260, A:K.260, A:K.260, A:K.260, A:K.260, A:R.264 Salt bridges: A:K.19, A:K.260, A:K.260, A:R.264 pi-Stacking: A:H.170, A:H.170

2 x AMZ: AMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE(Non-covalent)

AMZ.2: 14 residues within 4Å: Chain A: E.118, I.120, R.122, G.127, S.128, D.171, D.215, K.217, D.239, S.240, S.241, R.242, R.264 Ligands: ADP.5 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:S.128, A:D.171, A:D.171, A:K.217, A:D.239, A:S.240, A:S.241, A:R.264, A:R.264 Water bridges: A:S.128, A:N.173, A:N.173, A:N.173, A:S.241, A:S.241, A:R.242, A:R.242, A:K.260 Salt bridges: A:R.122, A:R.242 AMZ.3: 9 residues within 4Å: Chain A: E.62, K.66, L.76, V.77, I.79, S.106, L.107, L.108 Ligands: AMP.4 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:E.62, A:V.77, A:S.106, A:L.108, A:L.108 Water bridges: A:K.59, A:K.59, A:K.59, A:K.59, A:K.59, A:E.62, A:K.66, A:K.66, A:K.66, A:I.79 Salt bridges: A:K.66

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.4: 10 residues within 4Å: Chain A: E.62, K.66, L.76, V.77, I.79, I.85, S.106, L.107, L.108 Ligands: AMZ.3 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:E.62, A:V.77, A:L.108, A:L.108 Water bridges: A:K.59, A:K.59, A:K.59, A:K.59, A:K.59, A:E.62, A:K.66, A:K.66, A:K.66, A:I.79, A:I.85 Salt bridges: A:K.66

2 x SIN: SUCCINIC ACID(Non-covalent)

SIN.6: 3 residues within 4Å: Chain A: G.184, E.185, D.186 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.185 Hydrogen bonds: A:E.185, A:D.186, A:D.186 Water bridges: A:E.185 SIN.7: 5 residues within 4Å: Chain A: Y.42, K.131, R.242, Q.261, R.264 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.42 Hydrogen bonds: A:Q.261 Water bridges: A:Y.42, A:K.131, A:K.131, A:K.131, A:R.242, A:R.242, A:R.242 Salt bridges: A:K.131, A:R.242, A:R.264

1 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 2 residues within 4Å: Chain A: R.21 Ligands: ADP.1 No protein-ligand interaction detected (PLIP)

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

SO4.9: 3 residues within 4Å: Chain A: R.289, W.304, S.305 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.305 Water bridges: A:R.289, A:R.289 Salt bridges: A:R.289 SO4.10: 1 residues within 4Å: Chain A: K.225 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.225 SO4.11: 4 residues within 4Å: Chain A: R.73, N.74, L.76, H.110 9 PLIP interactions: 9 interactions with chain A Water bridges: A:R.73, A:R.73, A:R.73, A:R.73, A:R.73, A:R.73, A:N.74 Salt bridges: A:R.73, A:H.110 SO4.12: 3 residues within 4Å: Chain A: F.262, R.287, K.291 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.287, A:K.291, A:K.291, A:K.291 Salt bridges: A:R.287, A:K.291

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Urusova, D.V. et al., Saicar Synthase: Substrate Recognition, Conformational Flexibility and Catalysis. To be Published

Release Date

2006-06-08

Peptides

PHOSPHORIBOSYLAMINOIMIDAZOLE-SUCCINOCARBOXAMIDE SYNTHASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

PHOSPHORIBOSYLAMINOIMIDAZOLE-SUCCINOCARBOXAMIDE SYNTHASE

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