SMTL ID : 1kh3.1

Crystal Structure of Thermus thermophilus HB8 Argininosuccinate Synthetase in complex with inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: S.8, G.10, L.11, D.12, T.13 Ligands: ANP.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.8, A:G.10, A:G.10, A:D.12, A:T.13 Water bridges: A:D.12 SO4.12: 6 residues within 4Å: Chain B: S.8, G.10, L.11, D.12, T.13 Ligands: ANP.14 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.8, B:G.10, B:G.10, B:D.12, B:T.13 Water bridges: B:L.11, B:G.114 SO4.15: 7 residues within 4Å: Chain C: S.8, G.9, G.10, L.11, D.12, T.13 Ligands: ANP.17 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.8, C:G.10, C:G.10, C:D.12, C:T.13 Water bridges: C:D.12, C:G.114 SO4.18: 6 residues within 4Å: Chain D: S.8, G.10, L.11, D.12, T.13 Ligands: ANP.20 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.8, D:G.10, D:L.11, D:D.12, D:T.13 Water bridges: D:G.114

4 x MG: MAGNESIUM ION(Non-functional Binders)

MG.2: 1 residues within 4Å: Ligands: ANP.3 No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Ligands: ANP.14 No protein-ligand interaction detected (PLIP) MG.16: 1 residues within 4Å: Ligands: ANP.17 No protein-ligand interaction detected (PLIP) MG.19: 1 residues within 4Å: Ligands: ANP.20 No protein-ligand interaction detected (PLIP)

4 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.3: 19 residues within 4Å: Chain A: A.6, Y.7, T.13, F.31, T.32, A.33, Q.37, R.92, I.95, H.113, G.114, A.115, F.125, S.173, M.174 Ligands: SO4.1, MG.2, ARG.4, ASP.8 13 PLIP interactions: 11 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:A.6, A:A.33, A:A.33, A:R.92, A:R.92, A:G.114, A:G.114, A:M.174, A:M.174, R.4, D.8 Water bridges: A:Q.37 Salt bridges: A:R.92 ANP.14: 19 residues within 4Å: Chain B: A.6, Y.7, T.13, F.31, T.32, A.33, Q.37, R.92, I.95, H.113, G.114, A.115, F.125, S.173, M.174 Ligands: ARG.5, ASP.9, SO4.12, MG.13 11 PLIP interactions: 9 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: B:A.33, B:A.33, B:R.92, B:R.92, B:G.114, B:G.114, B:M.174, B:M.174, R.5, D.9 Salt bridges: B:R.92 ANP.17: 20 residues within 4Å: Chain C: A.6, Y.7, T.13, F.31, T.32, A.33, Q.37, R.92, I.95, H.113, G.114, A.115, F.125, S.173, M.174, D.175 Ligands: ARG.6, ASP.10, SO4.15, MG.16 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:A.6, C:A.33, C:A.33, C:R.92, C:R.92, C:G.114, C:G.114, C:M.174, C:M.174 Water bridges: C:D.12, C:D.12 Salt bridges: C:R.92 ANP.20: 20 residues within 4Å: Chain D: A.6, Y.7, T.13, F.31, T.32, A.33, Q.37, R.92, I.95, H.113, G.114, A.115, F.125, S.173, M.174, D.175 Ligands: ARG.7, ASP.11, SO4.18, MG.19 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:A.6, D:A.33, D:A.33, D:R.92, D:R.92, D:G.114, D:G.114, D:M.174, D:M.174 Water bridges: D:T.116 Salt bridges: D:R.92

4 x ARG: ARGININE(Non-covalent)

ARG.4: 15 residues within 4Å: Chain A: Y.84, T.88, S.89, N.120, R.124, S.173, M.174, D.175, S.182, Y.183, E.184, E.258, Y.270, Y.310 Ligands: ANP.3 14 PLIP interactions: 13 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:T.88 Hydrogen bonds: A:Y.84, A:Y.84, A:S.89, A:N.120, A:S.173, A:M.174, A:E.184, A:E.258 Water bridges: A:Y.183, A:Y.183, D.8 Salt bridges: A:R.124, A:E.184 ARG.5: 15 residues within 4Å: Chain B: Y.84, T.88, S.89, N.120, R.124, S.173, M.174, D.175, S.182, Y.183, E.184, E.258, Y.270, Y.310 Ligands: ANP.14 15 PLIP interactions: 13 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:T.88 Hydrogen bonds: B:Y.84, B:Y.84, B:S.89, B:N.120, B:S.173, B:S.173, B:E.184, B:E.258, B:Y.270 Water bridges: B:E.184, R.5, D.9 Salt bridges: B:R.124, B:E.184 ARG.6: 15 residues within 4Å: Chain C: Y.84, T.88, S.89, N.120, R.124, S.173, M.174, D.175, S.182, Y.183, E.184, E.258, Y.270, Y.310 Ligands: ANP.17 16 PLIP interactions: 14 interactions with chain C, 2 Ligand-Ligand interactions Hydrophobic interactions: C:T.88 Hydrogen bonds: C:Y.84, C:S.89, C:N.120, C:S.173, C:M.174, C:E.184, C:E.258, C:E.258, C:Y.310 Water bridges: C:E.184, C:Y.270, R.6, D.10 Salt bridges: C:R.124, C:E.184 ARG.7: 15 residues within 4Å: Chain D: Y.84, T.88, S.89, N.120, R.124, S.173, M.174, D.175, S.182, Y.183, E.184, E.258, Y.270, Y.310 Ligands: ANP.20 11 PLIP interactions: 11 interactions with chain D, Hydrogen bonds: D:T.88, D:S.89, D:N.120, D:S.173, D:S.173, D:E.184, D:E.258, D:Y.270, D:Y.310 Salt bridges: D:R.124, D:E.184

4 x ASP: ASPARTIC ACID(Non-covalent)

ASP.8: 7 residues within 4Å: Chain A: A.115, T.116, G.119, N.120, D.121, E.184 Ligands: ANP.3 11 PLIP interactions: 10 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:R.92, A:T.116, A:N.120, A:N.120, A:D.121, A:D.121 Water bridges: A:T.116, A:G.119, A:G.119, A:R.260, R.4 ASP.9: 7 residues within 4Å: Chain B: A.115, T.116, G.119, N.120, D.121, E.184 Ligands: ANP.14 13 PLIP interactions: 10 interactions with chain B, 3 Ligand-Ligand interactions Hydrogen bonds: B:T.116, B:N.120, B:N.120, B:D.121, B:D.121 Water bridges: B:T.116, B:G.119, B:G.119, B:R.260, R.5, D.9, D.9 Salt bridges: B:R.260 ASP.10: 7 residues within 4Å: Chain C: A.115, T.116, G.119, N.120, D.121, E.184 Ligands: ANP.17 11 PLIP interactions: 10 interactions with chain C, 1 Ligand-Ligand interactions Hydrogen bonds: C:T.116, C:G.119, C:N.120, C:N.120, C:D.121 Water bridges: C:T.116, C:T.116, C:Q.122, C:R.260, R.6 Salt bridges: C:R.260 ASP.11: 7 residues within 4Å: Chain D: A.115, T.116, G.119, N.120, D.121, E.184 Ligands: ANP.20 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:T.116, D:N.120, D:N.120, D:D.121, D:D.121 Water bridges: D:T.116, D:T.116, D:G.119, D:Q.122 Salt bridges: D:R.260

Links

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Citation

Goto, M. et al., Structures of Argininosuccinate Synthetase in Enzyme-ATP Substrates and Enzyme-AMP Product Forms: STEREOCHEMISTRY OF THE CATALYTIC REACTION. J.Biol.Chem. (2003)

Release Date

2003-04-22

Peptides

Argininosuccinate Synthetase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Argininosuccinate Synthetase

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