SMTL ID : 2gcq.1

Fully ligated E.Coli Adenylosuccinate Synthetase with GTP, 2'-deoxy-IMP and Hadacidin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 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: DOI.2, GDP.3, HDA.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.13, A:G.40, HDA.4 MG.5: 6 residues within 4Å: Chain B: D.13, G.40, R.305 Ligands: DOI.6, GDP.7, HDA.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.13, B:G.40, HDA.8

2 x DOI: 9-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-6-(PHOSPHONOOXY)-9H-PURINE(Non-covalent)

DOI.2: 24 residues within 4Å: Chain A: W.11, G.12, D.13, K.16, N.38, A.39, G.40, H.41, I.126, G.127, T.128, T.129, A.223, Q.224, L.228, V.238, T.239, V.273, G.274, R.303 Chain B: R.143 Ligands: MG.1, GDP.3, HDA.4 19 PLIP interactions: 18 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.13, A:N.38, A:G.40, A:I.126, A:T.129, A:Q.224, A:Q.224, A:T.239 Water bridges: A:D.114, A:T.129, A:G.134, A:G.134, A:T.239, A:S.240, A:R.272, A:R.272 Salt bridges: A:K.16, A:H.41, B:R.143 DOI.6: 24 residues within 4Å: Chain A: R.143 Chain B: W.11, G.12, D.13, K.16, N.38, A.39, G.40, H.41, I.126, G.127, T.128, T.129, A.223, Q.224, L.228, V.238, T.239, V.273, G.274, R.303 Ligands: MG.5, GDP.7, HDA.8 18 PLIP interactions: 17 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.13, B:N.38, B:G.40, B:I.126, B:T.129, B:Q.224, B:Q.224 Water bridges: B:T.129, B:T.129, B:G.134, B:G.134, B:T.239, B:S.240, B:R.272, B:R.272 Salt bridges: B:K.16, B:H.41, A:R.143

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

GDP.3: 21 residues within 4Å: Chain A: D.13, E.14, G.15, K.16, G.17, K.18, G.40, H.41, T.42, A.299, R.305, K.331, D.333, V.334, S.414, T.415, G.416, P.417 Ligands: MG.1, DOI.2, HDA.4 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:D.13, A:D.13, A:E.14, A:E.14, A:G.15, A:K.16, A:G.17, A:T.42, A:T.42, A:K.331, A:S.414, A:G.416 Water bridges: A:K.18, A:K.331, A:K.331 Salt bridges: A:K.16, A:H.41, A:R.305, A:D.333 GDP.7: 21 residues within 4Å: Chain B: D.13, E.14, G.15, K.16, G.17, K.18, G.40, H.41, T.42, A.299, R.305, K.331, D.333, V.334, S.414, T.415, G.416, P.417 Ligands: MG.5, DOI.6, HDA.8 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:D.13, B:E.14, B:G.15, B:K.16, B:G.17, B:T.42, B:T.42, B:K.331, B:S.414, B:G.416 Water bridges: B:K.18, B:K.331, B:K.331 Salt bridges: B:K.16, B:H.41, B:R.305, B:D.333

2 x HDA: HADACIDIN(Non-covalent)

HDA.4: 14 residues within 4Å: Chain A: D.13, N.38, G.40, T.129, V.273, G.298, A.299, T.300, T.301, R.303, R.305 Ligands: MG.1, DOI.2, GDP.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.13, A:G.298, A:A.299, A:T.300, A:T.301, A:G.302, A:R.305 Salt bridges: A:R.303 HDA.8: 14 residues within 4Å: Chain B: D.13, N.38, G.40, T.129, V.273, G.298, A.299, T.300, T.301, R.303, R.305 Ligands: MG.5, DOI.6, GDP.7 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:D.13, B:G.298, B:A.299, B:T.300, B:T.300, B:T.301, B:G.302, B:R.305 Salt bridges: B:R.303

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Iancu, C.V. et al., Cavitation as a mechanism of substrate discrimination by adenylosuccinate synthetases. Biochemistry (2006)

Release Date

2007-04-24

Peptides

Adenylosuccinate Synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Adenylosuccinate Synthetase

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