SMTL ID : 6yei.1

Arabidopsis thaliana glutamate dehydrogenase isoform 1 in complex with NAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

homo-hexamer

Ligands

6 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 16 residues within 4Å: Chain A: T.188, G.216, F.217, G.218, N.219, V.220, S.239, D.240, I.241, A.291, A.292, L.293, A.313, A.314, N.315, N.340 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:T.188, A:V.220, A:N.340 Hydrogen bonds: A:F.217, A:F.217, A:N.219, A:N.219, A:V.220, A:I.241, A:A.292, A:N.315, A:N.315 Water bridges: A:T.188, A:G.218, A:G.221 NAD.9: 15 residues within 4Å: Chain B: T.188, G.216, F.217, G.218, N.219, V.220, D.240, I.241, A.291, A.292, L.293, A.313, A.314, N.315, N.340 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:T.188, B:V.220 Hydrogen bonds: B:F.217, B:F.217, B:N.219, B:N.219, B:V.220, B:I.241, B:A.292, B:N.315, B:N.315 Water bridges: B:T.188, B:G.218, B:G.221 NAD.14: 16 residues within 4Å: Chain C: R.184, T.188, G.216, F.217, G.218, N.219, V.220, D.240, I.241, A.291, A.292, L.293, A.313, A.314, N.315, N.340 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:T.188, C:V.220 Hydrogen bonds: C:R.184, C:T.188, C:F.217, C:F.217, C:N.219, C:N.219, C:V.220, C:I.241, C:A.292, C:N.315, C:N.315 Water bridges: C:N.219 NAD.20: 15 residues within 4Å: Chain D: T.188, G.216, F.217, G.218, N.219, V.220, D.240, I.241, A.291, A.292, L.293, A.313, A.314, N.315, N.340 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:T.188, D:V.220 Hydrogen bonds: D:F.217, D:F.217, D:N.219, D:N.219, D:V.220, D:I.241, D:A.292, D:N.315, D:N.315 Water bridges: D:T.188, D:G.218, D:G.221 NAD.28: 18 residues within 4Å: Chain E: K.93, T.188, Q.215, G.216, F.217, G.218, N.219, V.220, S.239, D.240, I.241, A.291, A.292, L.293, A.313, A.314, N.315, N.340 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:T.188, E:N.340 Hydrogen bonds: E:T.188, E:F.217, E:F.217, E:N.219, E:N.219, E:V.220, E:G.221, E:I.241, E:N.315, E:N.315 Water bridges: E:T.188 NAD.33: 22 residues within 4Å: Chain F: R.73, D.145, M.146, G.147, R.184, T.188, Q.215, G.216, F.217, G.218, N.219, V.220, D.240, I.241, A.291, A.292, L.293, A.313, A.314, N.315, N.340 Ligands: AKG.34 23 PLIP interactions: 23 interactions with chain F Hydrophobic interactions: F:T.188, F:V.220, F:N.340 Hydrogen bonds: F:R.73, F:D.145, F:G.147, F:R.184, F:R.184, F:T.188, F:F.217, F:F.217, F:N.219, F:N.219, F:V.220, F:I.241, F:A.292, F:N.315, F:N.315 Water bridges: F:T.188, F:G.218, F:G.221, F:S.239, F:D.240

15 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 9 residues within 4Å: Chain A: Y.166, P.168, L.178, G.179, N.354, G.357, F.358, M.359 Chain E: P.100 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.354 MPD.3: 7 residues within 4Å: Chain A: E.37, K.39, F.57, V.59, V.78, P.80, V.83 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:K.39, A:F.57, A:F.57, A:V.78, A:V.83 Hydrogen bonds: A:E.37 MPD.4: 6 residues within 4Å: Chain A: E.202, H.203, V.332, C.384, C.389, L.391 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.202 Hydrogen bonds: A:H.203 MPD.5: 5 residues within 4Å: Chain A: S.222, W.223, K.226, L.257, K.261 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.223, A:K.226, A:L.257 Hydrogen bonds: A:K.261, A:K.261 MPD.10: 9 residues within 4Å: Chain B: Y.166, P.168, L.178, G.179, N.354, G.357, F.358, M.359 Chain D: P.100 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: D:P.100 Hydrogen bonds: B:Y.166, B:Y.166, B:N.354 MPD.11: 7 residues within 4Å: Chain B: E.37, K.39, F.57, V.59, V.78, P.80, V.83 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:K.39, B:F.57, B:V.78, B:V.83 Hydrogen bonds: B:E.37, B:E.37 MPD.12: 5 residues within 4Å: Chain B: L.199, E.202, H.203, C.384, L.391 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:E.202 MPD.15: 7 residues within 4Å: Chain A: P.100 Chain C: Y.166, P.168, G.179, N.354, G.357, F.358 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.166, C:Y.166, C:N.354 MPD.16: 6 residues within 4Å: Chain C: E.37, K.39, F.57, V.59, V.78, P.80 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:K.39, C:F.57, C:V.78, C:P.80 Hydrogen bonds: C:E.37 MPD.21: 6 residues within 4Å: Chain D: E.37, K.39, F.57, V.59, V.78, P.80 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:K.39, D:F.57, D:F.57, D:V.59, D:P.80 Hydrogen bonds: D:E.37 MPD.22: 10 residues within 4Å: Chain D: Y.166, P.168, D.177, L.178, G.179, N.354, G.357, F.358, M.359 Chain F: P.100 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:Y.166 Hydrogen bonds: D:Y.166, D:N.354 MPD.23: 4 residues within 4Å: Chain D: S.222, W.223, K.226, L.257 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:W.223, D:W.223, D:W.223, D:K.226, D:L.257 Hydrogen bonds: D:S.222, D:S.222 MPD.24: 4 residues within 4Å: Chain D: L.199, H.203, V.332, L.391 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:V.332 MPD.27: 7 residues within 4Å: Chain D: D.47, S.118, R.122 Chain E: K.46, D.47, G.49, R.122 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:D.47 Hydrogen bonds: D:S.118, D:S.118, D:R.122 Water bridges: D:D.47, D:S.118 MPD.29: 9 residues within 4Å: Chain E: E.37, I.38, K.39, F.57, V.59, V.78, P.80, N.84 Ligands: EDO.35 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:F.57, E:F.57, E:V.78, E:P.80 Hydrogen bonds: E:E.37

6 x K: POTASSIUM ION(Non-covalent)

K.6: 3 residues within 4Å: Chain A: S.30, I.33 Chain B: E.41 6 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:S.30, A:I.33, B:E.41, H2O.1, H2O.4, H2O.11 K.7: 3 residues within 4Å: Chain A: E.41 Chain B: S.30, I.33 6 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:E.41, B:S.30, B:I.33, H2O.8, H2O.10, H2O.11 K.18: 3 residues within 4Å: Chain C: S.30, I.33 Chain D: E.41 6 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: D:E.41, C:S.30, C:I.33, H2O.14, H2O.15, H2O.15 K.25: 3 residues within 4Å: Chain C: E.41 Chain D: S.30, I.33 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: D:S.30, D:I.33, C:E.41, H2O.19, H2O.20 K.30: 3 residues within 4Å: Chain E: S.30, I.33 Chain F: E.41 6 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: E:S.30, E:I.33, F:E.41, H2O.21, H2O.22, H2O.28 K.32: 3 residues within 4Å: Chain E: E.41 Chain F: S.30, I.33 6 PLIP interactions: 2 interactions with chain F, 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: F:S.30, F:I.33, E:E.41, H2O.24, H2O.27, H2O.28

5 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.8: 7 residues within 4Å: Chain A: Y.74, I.117, L.120, G.147, Q.151, T.152, W.155 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.74, A:I.117, A:L.120, A:Q.151, A:W.155 MRD.13: 7 residues within 4Å: Chain B: Y.74, I.117, L.120, G.147, Q.151, T.152, W.155 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.74, B:I.117, B:L.120 Water bridges: B:T.152 MRD.17: 7 residues within 4Å: Chain C: Y.74, I.117, L.120, G.147, Q.151, T.152, W.155 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Y.74, C:I.117, C:L.120 Water bridges: C:T.152, C:T.152 MRD.26: 7 residues within 4Å: Chain D: Y.74, I.117, L.120, G.147, Q.151, T.152, W.155 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:Y.74, D:I.117, D:L.120, D:Q.151, D:W.155 Hydrogen bonds: D:G.149, D:T.152, D:T.152 MRD.31: 7 residues within 4Å: Chain E: Y.74, I.117, L.120, G.147, Q.151, T.152, W.155 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:Y.74, E:I.117, E:L.120

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

EDO.19: 4 residues within 4Å: Chain D: D.47, G.49 Chain E: S.118, R.122 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.122 Water bridges: E:S.118 EDO.35: 3 residues within 4Å: Chain F: E.37, P.80 Ligands: MPD.29 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:E.37, F:E.37

1 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.34: 14 residues within 4Å: Chain F: K.69, G.71, M.90, K.93, K.105, A.143, D.145, T.172, R.184, N.315, G.343, V.344, S.347 Ligands: NAD.33 12 PLIP interactions: 12 interactions with chain F Hydrophobic interactions: F:A.143 Hydrogen bonds: F:G.71, F:D.145, F:T.172, F:N.315, F:S.347 Water bridges: F:K.93, F:K.105 Salt bridges: F:K.69, F:K.93, F:K.105, F:R.184

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grzechowiak, M. et al., Structural Studies of Glutamate Dehydrogenase (Isoform 1) FromArabidopsis thaliana, an Important Enzyme at the Branch-Point Between Carbon and Nitrogen Metabolism. Front Plant Sci (2020)

Release Date

2020-05-20

Peptides

Glutamate dehydrogenase 1: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Glutamate dehydrogenase 1

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