SMTL ID : 1qf5.1

DESIGN, SYNTHESIS, AND X-RAY CRYSTAL STRUCTURE OF AN ENZYME BOUND BISUBSTRATE HYBRID INHIBITOR OF ADENYLOSUCCINATE SYNTHETASE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 11 residues within 4Å: Chain A: G.12, D.13, K.16, A.39, G.40, H.41, A.223, Q.224 Ligands: MG.2, GDP.3, RPL.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.13, A:G.40, A:G.40, A:Q.224, A:Q.224 Salt bridges: A:K.16, A:H.41 PO4.5: 11 residues within 4Å: Chain B: G.12, D.13, K.16, A.39, G.40, H.41, A.223, Q.224 Ligands: MG.6, GDP.7, RPL.8 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.13, B:G.40, B:G.40, B:Q.224, B:Q.224 Salt bridges: B:K.16, B:H.41

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.13, G.40 Ligands: PO4.1, GDP.3, RPL.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.13, A:G.40 MG.6: 5 residues within 4Å: Chain B: D.13, G.40 Ligands: PO4.5, GDP.7, RPL.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.13, B:G.40

2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.3: 20 residues within 4Å: Chain A: D.13, E.14, G.15, K.16, G.17, K.18, G.40, H.41, T.42, R.305, K.331, D.333, V.334, S.414, T.415, G.416, P.417 Ligands: PO4.1, MG.2, RPL.4 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:E.14, A:G.15, A:K.16, A:G.17, A:G.40, A:T.42, A:T.42, A:T.42, A:K.331, A:K.331, A:S.414, A:G.416 Water bridges: A:K.18, A:R.305, A:R.305 Salt bridges: A:K.16, A:H.41, A:R.305, A:D.333 GDP.7: 20 residues within 4Å: Chain B: D.13, E.14, G.15, K.16, G.17, K.18, G.40, H.41, T.42, R.305, K.331, D.333, V.334, S.414, T.415, G.416, P.417 Ligands: PO4.5, MG.6, RPL.8 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:E.14, B:E.14, B:G.15, B:K.16, B:G.17, B:G.40, B:T.42, B:T.42, B:T.42, B:K.331, B:K.331, B:S.414, B:G.416 Water bridges: B:K.18, B:R.305, B:R.305 Salt bridges: B:K.16, B:H.41, B:R.305, B:D.333

2 x RPL: (C8-S)-HYDANTOCIDIN 5'-PHOSPHATE(Non-covalent)

RPL.4: 22 residues within 4Å: Chain A: D.13, N.38, G.40, G.127, T.128, T.129, Q.224, L.228, V.238, T.239, V.273, G.274, G.298, A.299, T.300, T.301, R.303, R.305 Chain B: R.143 Ligands: PO4.1, MG.2, GDP.3 27 PLIP interactions: 26 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.273 Hydrogen bonds: A:N.38, A:G.40, A:G.40, A:G.127, A:T.129, A:Q.224, A:G.298, A:A.299, A:T.300, A:T.300, A:T.301, A:G.302, A:R.303, A:R.303, A:R.305 Water bridges: A:D.114, A:T.129, A:T.129, A:G.134, A:Y.237, A:S.240, A:R.272, A:A.275 Salt bridges: A:D.13, A:R.303, B:R.143 RPL.8: 22 residues within 4Å: Chain A: R.143 Chain B: D.13, N.38, G.40, G.127, T.128, T.129, Q.224, L.228, V.238, T.239, V.273, G.274, G.298, A.299, T.300, T.301, R.303, R.305 Ligands: PO4.5, MG.6, GDP.7 28 PLIP interactions: 25 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:V.273 Hydrogen bonds: B:N.38, B:G.40, B:G.40, B:G.127, B:T.129, B:Q.224, B:T.239, B:G.298, B:A.299, B:T.300, B:T.301, B:G.302, B:R.303, B:R.303, B:R.305 Water bridges: B:D.114, B:T.129, B:I.133, B:G.134, B:Y.237, B:R.272, B:A.275, A:R.143, A:R.143 Salt bridges: B:D.13, B:R.303, A:R.143

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hanessian, S. et al., An enzyme-bound bisubstrate hybrid inhibitor of adenylosuccinate synthetase. Angew.Chem.Int.Ed.Engl. (1999)

Release Date

1999-12-02

Peptides

PROTEIN (ADENYLOSUCCINATE SYNTHETASE): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

PROTEIN (ADENYLOSUCCINATE SYNTHETASE)

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