SMTL ID : 3zzf.1

Crystal structure of the amino acid kinase domain from Saccharomyces cerevisiae acetylglutamate kinase complexed with its substrate N- acetylglutamate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

13 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 5 residues within 4Å: Chain A: L.154, G.163, V.199, N.200, V.203 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.200 Water bridges: A:N.164 EDO.2: 7 residues within 4Å: Chain A: L.215, K.216, I.217, V.218, S.276, A.278, E.288 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.217, A:S.276, A:E.288 EDO.3: 2 residues within 4Å: Chain A: N.221, K.260 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.221 Water bridges: A:K.54, A:E.222 EDO.4: 5 residues within 4Å: Chain A: D.62, N.63, L.64, H.65, E.66 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.64, A:H.65, A:E.66, A:E.66 Water bridges: A:D.62 EDO.11: 6 residues within 4Å: Chain B: L.154, G.163, V.199, N.200, V.203 Ligands: NLG.20 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.200 Water bridges: B:N.164 EDO.12: 4 residues within 4Å: Chain B: Y.153, T.191, S.193, Q.195 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.153, B:Y.153, B:T.191, B:S.193 Water bridges: B:S.193 EDO.13: 5 residues within 4Å: Chain B: R.33, Q.37, K.40, Y.41, L.215 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.33, B:Q.37 Water bridges: B:E.36 EDO.14: 6 residues within 4Å: Chain B: S.20, T.21, Q.24, A.72, F.73, H.76 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.20, B:Q.24, B:H.76 EDO.15: 6 residues within 4Å: Chain B: Y.41, Q.48, Q.49, F.50, Y.80, I.177 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.48, B:Q.49, B:F.50, B:Y.80 Water bridges: B:A.51 EDO.16: 4 residues within 4Å: Chain B: Y.104, G.107, Y.255, G.256 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.107, B:G.256 Water bridges: B:N.200, B:N.200 EDO.24: 4 residues within 4Å: Chain C: E.171, E.174, A.175, K.178 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.171 EDO.25: 4 residues within 4Å: Chain C: N.221, E.222, K.223 Ligands: GOL.26 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.222, C:K.223, C:K.223 Water bridges: C:G.56 EDO.31: 6 residues within 4Å: Chain D: S.20, T.21, Q.24, A.72, F.73, H.76 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.24, D:A.72, D:H.76

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: Y.104, G.107, G.256 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.200, A:N.200, A:G.256 GOL.17: 4 residues within 4Å: Chain B: K.54, G.56, N.221, K.260 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:K.54, B:N.221 Water bridges: B:K.54, B:K.54, B:D.202, B:D.202, B:E.222, B:E.222, B:K.223, B:G.225, B:K.260, B:K.260 GOL.26: 6 residues within 4Å: Chain C: K.54, G.56, N.221, K.223, K.260 Ligands: EDO.25 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:K.54, C:N.221, C:K.223 Water bridges: C:K.54, C:K.54, C:G.56, C:N.200, C:K.260, C:K.260 GOL.32: 3 residues within 4Å: Chain D: K.54, N.221, K.260 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:N.221, D:K.260, D:K.260 Water bridges: D:K.54, D:K.54, D:G.57, D:E.222

8 x HG: MERCURY (II) ION(Non-covalent)

HG.6: 4 residues within 4Å: Chain A: C.70, L.74, Q.286 Ligands: CL.10 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.70 HG.7: 6 residues within 4Å: Chain A: R.94, V.118, K.121, C.122, E.125 Ligands: CL.9 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.122 HG.18: 3 residues within 4Å: Chain B: C.70, L.74, Q.286 No protein-ligand interaction detected (PLIP) HG.19: 6 residues within 4Å: Chain B: R.94, V.118, K.121, C.122 Ligands: CL.21, CL.22 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.122 HG.27: 3 residues within 4Å: Chain C: C.70, L.74, Q.286 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:C.70 HG.28: 5 residues within 4Å: Chain C: R.94, V.118, K.121, C.122 Ligands: CL.30 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.122, H2O.240 HG.33: 3 residues within 4Å: Chain D: E.66, C.70 Ligands: CL.36 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.70, H2O.334 HG.34: 4 residues within 4Å: Chain D: R.94, V.118, K.121, C.122 No protein-ligand interaction detected (PLIP)

4 x NLG: N-ACETYL-L-GLUTAMATE(Non-covalent)

NLG.8: 10 residues within 4Å: Chain A: G.86, T.87, G.88, I.108, R.109, F.123, N.198, V.199, N.200, A.201 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:T.87, A:I.108, A:F.123 Hydrogen bonds: A:T.87, A:G.88, A:R.109, A:N.198, A:N.198, A:N.198, A:N.200, A:A.201 Water bridges: A:K.54, A:K.54, A:G.57, A:D.202 Salt bridges: A:K.54, A:R.109 NLG.20: 10 residues within 4Å: Chain B: G.86, T.87, G.88, R.109, F.123, N.198, V.199, N.200, A.201 Ligands: EDO.11 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:F.123 Hydrogen bonds: B:T.87, B:G.88, B:Y.104, B:R.109, B:N.198, B:N.198, B:N.198, B:A.201 Water bridges: B:K.54, B:K.54, B:N.200, B:D.202 Salt bridges: B:K.54, B:R.109 NLG.29: 12 residues within 4Å: Chain C: G.86, T.87, G.88, Y.104, I.108, R.109, V.119, F.123, N.198, V.199, N.200, A.201 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:I.108, C:F.123 Hydrogen bonds: C:T.87, C:G.88, C:R.109, C:N.198, C:N.198, C:A.201 Water bridges: C:K.54, C:K.54, C:D.202 Salt bridges: C:K.54, C:R.109 NLG.35: 9 residues within 4Å: Chain D: G.86, T.87, G.88, I.108, R.109, N.198, V.199, N.200, A.201 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:I.108 Hydrogen bonds: D:T.87, D:G.88, D:Y.104, D:R.109, D:N.198, D:N.198, D:A.201 Water bridges: D:K.54, D:K.54, D:R.109, D:N.200, D:D.202 Salt bridges: D:K.54, D:R.109

7 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 4 residues within 4Å: Chain A: R.94, V.118, K.121 Ligands: HG.7 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: C.70, Q.286 Ligands: HG.6 Ligand excluded by PLIP CL.21: 6 residues within 4Å: Chain B: R.94, K.121, C.122, E.125 Ligands: HG.19, CL.22 Ligand excluded by PLIP CL.22: 5 residues within 4Å: Chain B: R.94, V.118, K.121 Ligands: HG.19, CL.21 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain B: E.66, S.69 Ligand excluded by PLIP CL.30: 4 residues within 4Å: Chain C: R.94, C.122, E.125 Ligands: HG.28 Ligand excluded by PLIP CL.36: 3 residues within 4Å: Chain D: E.66, S.69 Ligands: HG.33 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

De Cima, S. et al., Insight on an Arginine Synthesis Metabolon from the Tetrameric Structure of Yeast Acetylglutamate Kinase. Plos One (2012)

Release Date

2012-05-02

Peptides

ACETYLGLUTAMATE KINASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

ACETYLGLUTAMATE KINASE

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