SMTL ID : 1juy.1

REFINED CRYSTAL STRUCTURE OF ADENYLOSUCCINATE SYNTHETASE FROM ESCHERICHIA COLI COMPLEXED WITH HYDANTOCIDIN 5'-PHOSPHATE GDP, HPO4(2-), MG2+, AND HADACIDIN

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: D.13, G.40, R.305 Ligands: PI.2, GDP.3, HDA.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.13, A:G.40, HDA.5 MG.6: 6 residues within 4Å: Chain B: D.13, G.40, R.305 Ligands: PI.7, GDP.8, HDA.10 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.13, B:G.40, HDA.10

2 x PI: HYDROGENPHOSPHATE ION(Non-covalent)

PI.2: 13 residues within 4Å: Chain A: G.12, D.13, K.16, N.38, A.39, G.40, H.41, A.223, Q.224 Ligands: MG.1, GDP.3, H5P.4, HDA.5 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.13, A:N.38, A:G.40, A:G.40, A:Q.224, A:Q.224 Salt bridges: A:K.16, A:H.41 PI.7: 13 residues within 4Å: Chain B: G.12, D.13, K.16, N.38, A.39, G.40, H.41, A.223, Q.224 Ligands: MG.6, GDP.8, H5P.9, HDA.10 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:D.13, B:D.13, B:N.38, B:G.40, B:G.40, B:Q.224, B:Q.224 Salt bridges: B:K.16, B:H.41

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

GDP.3: 24 residues within 4Å: Chain A: D.13, E.14, G.15, K.16, G.17, K.18, G.40, H.41, T.42, V.44, N.295, A.299, R.305, K.331, D.333, V.334, F.383, S.414, T.415, G.416, P.417 Ligands: MG.1, PI.2, HDA.5 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:D.13, A:G.15, A:K.16, A:G.17, A:G.40, A:T.42, A:T.42, A:K.331, A:K.331, A:S.414, A:G.416 Water bridges: A:G.294, A:N.295, A:R.305, A:R.305, A:R.305, A:R.305, A:P.417 Salt bridges: A:K.16, A:H.41, A:R.305, A:D.333 GDP.8: 24 residues within 4Å: Chain B: D.13, E.14, G.15, K.16, G.17, K.18, G.40, H.41, T.42, V.44, N.295, A.299, R.305, K.331, D.333, V.334, F.383, S.414, T.415, G.416, P.417 Ligands: MG.6, PI.7, HDA.10 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:D.13, B:D.13, B:G.15, B:K.16, B:G.17, B:G.40, B:T.42, B:T.42, B:K.331, B:K.331, B:S.414, B:G.416 Water bridges: B:G.294, B:N.295, B:R.305, B:R.305, B:R.305, B:R.305, B:P.417 Salt bridges: B:K.16, B:H.41, B:R.305, B:D.333

2 x H5P: HYDANTOCIDIN-5'-PHOSPHATE(Non-covalent)

H5P.4: 21 residues within 4Å: Chain A: N.38, I.126, G.127, T.128, T.129, G.130, I.133, G.134, Q.224, L.228, V.238, T.239, S.240, R.272, V.273, G.274, A.275, R.303 Chain B: R.143 Ligands: PI.2, HDA.5 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.38, A:I.126, A:T.128, A:T.129, A:T.129, A:Q.224, A:T.239, A:V.273, A:R.303 Water bridges: A:D.13, A:G.130, A:G.130, A:G.134, A:R.272, A:V.273, A:V.273, A:A.275 Salt bridges: B:R.143 H5P.9: 21 residues within 4Å: Chain A: R.143 Chain B: N.38, I.126, G.127, T.128, T.129, G.130, I.133, G.134, Q.224, L.228, V.238, T.239, S.240, R.272, V.273, G.274, A.275, R.303 Ligands: PI.7, HDA.10 18 PLIP interactions: 17 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.38, B:I.126, B:T.128, B:T.129, B:T.129, B:Q.224, B:T.239, B:V.273, B:R.303 Water bridges: B:D.13, B:G.130, B:G.130, B:G.134, B:R.272, B:V.273, B:V.273, B:A.275 Salt bridges: A:R.143

2 x HDA: HADACIDIN(Non-covalent)

HDA.5: 16 residues within 4Å: Chain A: D.13, N.38, G.40, T.129, V.273, G.298, A.299, T.300, T.301, G.302, R.303, R.305 Ligands: MG.1, PI.2, GDP.3, H5P.4 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:D.13, A:G.40, A:G.298, A:A.299, A:T.300, A:T.301, A:T.301, A:G.302, A:R.305 Salt bridges: A:D.13, A:R.303 HDA.10: 16 residues within 4Å: Chain B: D.13, N.38, G.40, T.129, V.273, G.298, A.299, T.300, T.301, G.302, R.303, R.305 Ligands: MG.6, PI.7, GDP.8, H5P.9 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:D.13, B:G.40, B:G.298, B:A.299, B:T.300, B:T.301, B:T.301, B:G.302, B:R.305 Salt bridges: B:D.13, B:R.303

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Poland, B.W. et al., Refined crystal structure of adenylosuccinate synthetase from Escherichia coli complexed with hydantocidin 5'-phosphate, GDP, HPO4(2-), Mg2+, and hadacidin. Biochemistry (1996)

Release Date

1997-06-24

Peptides

ADENYLOSUCCINATE SYNTHETASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

ADENYLOSUCCINATE SYNTHETASE

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