SMTL ID : 3zzh.1

Crystal structure of the amino acid kinase domain from Saccharomyces cerevisiae acetylglutamate kinase in complex with its feed- back inhibitor L-arginine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 7 residues within 4Å: Chain A: R.120, L.124, T.145, T.186, L.188, M.196 Chain B: S.146 Ligand excluded by PLIP EDO.2: 3 residues within 4Å: Chain A: N.27 Chain D: L.39, T.43 Ligand excluded by PLIP EDO.3: 6 residues within 4Å: Chain A: L.215, K.216, I.217, V.218, S.276, E.288 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: Y.104, I.105, D.106, G.107, Y.255 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: Y.153, T.191, S.193, Q.195 Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain A: V.203, G.206, E.207, R.210, E.263, E.266, L.267 Ligand excluded by PLIP EDO.10: 1 residues within 4Å: Chain B: R.33 Ligand excluded by PLIP EDO.11: 7 residues within 4Å: Chain A: S.146, G.147 Chain B: R.120, F.123, L.124, L.188, M.196 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain B: S.20, T.21, A.72, F.73, H.76 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: L.124 Chain B: G.147, T.150, T.169 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: T.132, Q.136 Chain B: K.178, A.179 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain B: E.36, L.39 Chain C: I.23, N.27 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain B: Y.41, E.213, P.214, L.215, P.272, S.275 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain B: Q.47, Q.48, Q.49, K.170, V.211, F.212 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain B: N.221, K.223, K.260 Ligands: EDO.23 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain B: D.112, E.113, K.160 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain B: Q.47, Q.49, E.174, I.177, K.178 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain B: G.224, K.234, N.281, Q.283, D.284, G.296 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain B: S.236, G.294, A.295, G.296, M.298 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain B: K.54, D.202, K.260 Ligands: EDO.18 Ligand excluded by PLIP EDO.24: 3 residues within 4Å: Chain B: L.64, H.65, A.133 Ligand excluded by PLIP EDO.25: 2 residues within 4Å: Chain B: D.152, T.191 Ligand excluded by PLIP EDO.30: 4 residues within 4Å: Chain C: D.103, Y.104, I.105, I.110 Ligand excluded by PLIP EDO.31: 6 residues within 4Å: Chain C: L.124, N.127, L.128, P.143, T.145 Chain D: P.172 Ligand excluded by PLIP EDO.32: 7 residues within 4Å: Chain C: K.54, G.56, A.58, I.59, L.220, N.221, E.222 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain C: D.62, N.63, L.64, H.65, E.66 Ligand excluded by PLIP EDO.34: 3 residues within 4Å: Chain B: R.19 Chain C: G.14, F.15 Ligand excluded by PLIP EDO.35: 7 residues within 4Å: Chain C: L.95, I.100, E.101, P.102, D.103, D.112, T.115 Ligand excluded by PLIP EDO.36: 7 residues within 4Å: Chain C: R.120, F.123, L.124, L.188, M.196 Chain D: S.146, G.147 Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain C: T.18, S.20, H.76, L.137 Ligand excluded by PLIP EDO.41: 5 residues within 4Å: Chain D: G.14, F.15, S.16, Y.75, H.76 Ligand excluded by PLIP EDO.42: 4 residues within 4Å: Chain D: T.21, A.72, F.73, H.76 Ligand excluded by PLIP EDO.43: 7 residues within 4Å: Chain D: K.223, G.224, K.234, N.281, Q.283, D.284, G.296 Ligand excluded by PLIP EDO.44: 4 residues within 4Å: Chain D: V.168, T.169, K.170, E.171 Ligand excluded by PLIP EDO.45: 5 residues within 4Å: Chain D: N.28, I.29, S.30, E.34, T.291 Ligand excluded by PLIP EDO.46: 1 residues within 4Å: Chain D: G.99 Ligand excluded by PLIP EDO.47: 8 residues within 4Å: Chain D: L.95, I.100, E.101, P.102, D.103, R.109, I.110, T.115 Ligand excluded by PLIP EDO.48: 6 residues within 4Å: Chain D: V.203, L.259, R.262, E.263, E.266 Ligands: MLI.58 Ligand excluded by PLIP EDO.49: 5 residues within 4Å: Chain D: K.234, I.235, S.236, M.237 Ligands: EDO.50 Ligand excluded by PLIP EDO.50: 6 residues within 4Å: Chain D: N.228, T.231, E.233, K.234, I.235 Ligands: EDO.49 Ligand excluded by PLIP EDO.51: 5 residues within 4Å: Chain D: S.236, G.294, A.295, G.296, M.298 Ligand excluded by PLIP EDO.52: 3 residues within 4Å: Chain C: K.178 Chain D: T.132, Q.136 Ligand excluded by PLIP EDO.53: 4 residues within 4Å: Chain D: K.54, P.89, D.202, K.260 Ligand excluded by PLIP EDO.54: 4 residues within 4Å: Chain D: S.46, Q.49, Y.80, I.177 Ligand excluded by PLIP EDO.55: 3 residues within 4Å: Chain D: T.18, T.21, H.76 Ligand excluded by PLIP

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

CL.7: 3 residues within 4Å: Chain A: G.224, K.234, G.296 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain B: A.58, N.221, E.222 Ligand excluded by PLIP CL.39: 2 residues within 4Å: Chain C: P.89, N.92 Ligand excluded by PLIP CL.56: 2 residues within 4Å: Chain D: N.221, E.222 Ligand excluded by PLIP CL.57: 4 residues within 4Å: Chain C: S.146, G.147 Chain D: R.120, M.196 Ligand excluded by PLIP

3 x MLI: MALONATE ION(Non-functional Binders)

MLI.8: 10 residues within 4Å: Chain A: I.108, L.154, V.162, G.163, N.164, V.199, N.200, V.203, L.259 Ligands: NLG.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.164, A:N.200 MLI.27: 8 residues within 4Å: Chain B: I.108, L.154, V.162, G.163, N.164, V.199, N.200 Ligands: NLG.28 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.164, B:N.200 Water bridges: B:G.163 MLI.58: 10 residues within 4Å: Chain D: I.108, L.154, V.162, G.163, N.164, V.199, N.200, L.259 Ligands: EDO.48, NLG.59 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.164, D:N.200

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

NLG.9: 11 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 Ligands: MLI.8 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: 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:A.201 Water bridges: A:K.54, A:R.109, A:N.200, A:D.202 Salt bridges: A:K.54, A:R.109 NLG.28: 11 residues within 4Å: Chain B: G.86, T.87, G.88, I.108, R.109, F.123, N.198, V.199, N.200, A.201 Ligands: MLI.27 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:T.87, B:I.108, B:F.123 Hydrogen bonds: B:T.87, B:G.88, B:Y.104, B:R.109, B:N.198, B:N.198, B:A.201 Water bridges: B:K.54, B:K.54, B:N.200 Salt bridges: B:K.54, B:R.109 NLG.40: 10 residues within 4Å: Chain C: G.86, T.87, G.88, I.108, R.109, F.123, N.198, V.199, N.200, A.201 10 PLIP interactions: 10 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:N.198, C:A.201 Salt bridges: C:R.109 NLG.59: 11 residues within 4Å: Chain D: G.86, T.87, G.88, I.108, R.109, F.123, N.198, V.199, N.200, A.201 Ligands: MLI.58 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:I.108, D:F.123 Hydrogen bonds: D:T.87, D:G.88, D:Y.104, D:R.109, D:N.198, D:N.198, D:N.198, D:A.201 Water bridges: D:K.54, D:K.54, D:N.200 Salt bridges: D:K.54, D:R.109

1 x ARG: ARGININE(Non-covalent)

ARG.29: 13 residues within 4Å: Chain C: Y.38, K.216, S.236, M.237, E.288, L.289, F.290, T.291, D.292, S.293, G.294, G.296, M.298 10 PLIP interactions: 9 interactions with chain C, 1 Ligand-Ligand interactions Hydrogen bonds: C:S.236, C:S.236, C:E.288, C:L.289, C:T.291, C:G.296, C:M.298, R.29 Salt bridges: C:K.216, C:E.288

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.38: 4 residues within 4Å: Chain C: T.191, A.192, S.193 Chain D: E.113 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:E.113, C:A.192, C:S.193, C:S.193

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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