SMTL ID : 3c1m.1 (2 other biounits)

Cyrstal Structure of threonine-sensitive aspartokinase from Methanococcus jannaschii with MgAMP-PNP and L-aspartate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

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

MG.1: 1 residues within 4Å: Ligands: ANP.3 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Ligands: ANP.10 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain C: K.266 Ligands: ANP.13 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Chain D: D.211 Ligands: ANP.17 No protein-ligand interaction detected (PLIP)

4 x ASP: ASPARTIC ACID(Non-covalent)

ASP.2: 9 residues within 4Å: Chain A: S.40, T.46, E.130, F.193, R.207, G.208, G.209, S.210 Ligands: ANP.3 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.193 Hydrogen bonds: A:S.40, A:A.41, A:T.46, A:E.130, A:G.208, A:S.210, A:S.210 Water bridges: A:K.6, A:G.9, A:D.211 Salt bridges: A:K.6, A:R.207 ASP.9: 9 residues within 4Å: Chain B: S.40, T.46, E.130, F.193, R.207, G.208, G.209, S.210 Ligands: ANP.10 15 PLIP interactions: 13 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:F.193 Hydrogen bonds: B:S.40, B:E.130, B:G.208, B:S.210, B:S.210, D.9, D.9 Water bridges: B:K.6, B:A.41, B:T.46, B:E.130, B:D.211 Salt bridges: B:K.6, B:R.207 ASP.12: 9 residues within 4Å: Chain C: S.40, T.46, E.130, F.193, R.207, G.208, G.209, S.210 Ligands: ANP.13 15 PLIP interactions: 4 Ligand-Ligand interactions, 11 interactions with chain C Hydrogen bonds: D.12, D.12, D.12, D.12, C:S.40, C:T.46, C:G.208, C:G.209, C:S.210, C:S.210 Water bridges: C:K.6, C:K.6, C:N.47 Salt bridges: C:K.6, C:R.207 ASP.16: 9 residues within 4Å: Chain D: S.40, T.46, E.130, F.193, R.207, G.208, G.209, S.210 Ligands: ANP.17 14 PLIP interactions: 1 Ligand-Ligand interactions, 13 interactions with chain D Hydrogen bonds: D.16, D:S.40, D:T.46, D:E.130, D:G.208, D:G.208, D:S.210 Hydrophobic interactions: D:F.193 Water bridges: D:K.6, D:T.46, D:T.46, D:D.211 Salt bridges: D:K.6, D:R.207

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

ANP.3: 20 residues within 4Å: Chain A: K.6, G.8, G.9, S.40, W.229, T.230, D.231, V.232, G.234, V.235, Y.236, T.238, D.239, P.240, R.241, A.265, K.266, V.267 Ligands: MG.1, ASP.2 22 PLIP interactions: 20 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:K.6, A:G.9, A:S.40, A:T.230, A:D.231, A:Y.236, A:Y.236, A:R.241, A:R.241, A:K.266, D.2, D.2 Water bridges: A:T.10, A:T.10, A:T.10, A:T.10, A:S.11, A:G.208, A:D.211, A:D.239, A:D.239 Salt bridges: A:K.266 ANP.10: 20 residues within 4Å: Chain B: K.6, G.8, G.9, S.40, D.211, T.230, D.231, V.232, G.234, V.235, Y.236, T.238, D.239, P.240, R.241, A.265, K.266, V.267 Ligands: MG.8, ASP.9 23 PLIP interactions: 21 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: B:K.6, B:K.6, B:G.9, B:S.40, B:T.230, B:D.231, B:Y.236, B:Y.236, B:R.241, B:K.266, D.9, D.9 Water bridges: B:G.8, B:G.8, B:T.10, B:T.10, B:D.211, B:D.239, B:D.239, B:K.266, B:K.266, B:K.266 Salt bridges: B:K.266 ANP.13: 20 residues within 4Å: Chain C: K.6, G.8, G.9, S.40, D.211, T.230, D.231, V.232, G.234, V.235, Y.236, T.238, D.239, P.240, R.241, A.265, K.266, V.267 Ligands: MG.11, ASP.12 21 PLIP interactions: 16 interactions with chain C, 5 Ligand-Ligand interactions Hydrogen bonds: C:K.6, C:K.6, C:G.9, C:S.40, C:D.231, C:Y.236, C:Y.236, C:R.241, C:R.241, C:K.266, D.12, D.12 Water bridges: C:G.8, C:G.8, C:T.10, C:T.10, C:T.10, D.12, D.12, D.12 Salt bridges: C:K.266 ANP.17: 20 residues within 4Å: Chain D: K.6, G.8, G.9, S.40, W.229, T.230, D.231, V.232, G.234, V.235, Y.236, T.238, D.239, P.240, R.241, A.265, K.266, V.267 Ligands: MG.15, ASP.16 23 PLIP interactions: 20 interactions with chain D, 3 Ligand-Ligand interactions Hydrogen bonds: D:K.6, D:K.6, D:G.9, D:S.40, D:T.230, D:D.231, D:Y.236, D:Y.236, D:R.241, D:R.241, D:K.266, D.16, D.16 Water bridges: D:T.10, D:T.10, D:T.10, D:S.11, D:G.208, D:D.211, D:D.239, D:D.239, D.16 Salt bridges: D:K.266

6 x FMT: FORMIC ACID(Non-functional Binders)

FMT.4: 3 residues within 4Å: Chain A: T.2, D.32, D.34 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.2, A:T.2 FMT.5: 4 residues within 4Å: Chain A: E.81, E.82, A.83, K.85 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.82 FMT.6: 1 residues within 4Å: Chain A: E.155 No protein-ligand interaction detected (PLIP) FMT.7: 4 residues within 4Å: Chain A: S.307, K.466, F.467, K.470 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.466 FMT.14: 6 residues within 4Å: Chain C: L.126, G.165, F.193, T.204, G.206, R.207 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.204, C:G.206 Water bridges: C:R.207 FMT.18: 3 residues within 4Å: Chain D: E.82, I.84, K.85 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:I.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, X. et al., The Structural Basis for Allosteric Inhibition of a Threonine-sensitive Aspartokinase. J.Biol.Chem. (2008)

Release Date

2008-03-25

Peptides

Probable aspartokinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Probable aspartokinase

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