SMTL ID : 8owm.1

Crystal structure of glutamate dehydrogenase 2 from Arabidopsis thaliana binding Ca, NAD and 2,2-dihydroxyglutarate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-hexamer

Ligands

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

NAD.1: 22 residues within 4Å: Chain A: 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, C.291, A.292, A.313, A.314, N.315, N.340 Ligands: GOL.2, U5C.8 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:T.188, A:V.220 Hydrogen bonds: A:R.73, A:D.145, A:G.147, A:R.184, A:R.184, A:T.188, 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:R.113, A:T.148, A:T.188, A:G.218, A:G.221, A:D.240, A:K.260 NAD.12: 23 residues within 4Å: Chain B: R.73, D.145, M.146, G.147, R.184, T.188, Q.215, G.216, F.217, G.218, N.219, V.220, S.239, D.240, I.241, C.291, A.292, A.313, A.314, N.315, N.340 Ligands: GOL.14, U5C.25 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:T.188, B:V.220, B:N.340 Hydrogen bonds: B:R.73, B:D.145, B:G.147, B:R.184, B:R.184, B:T.188, 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:Q.215, B:Q.215, B:G.218, B:G.221, B:D.240, B:D.240 NAD.28: 22 residues within 4Å: Chain C: 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, C.291, A.292, A.313, A.314, N.315, N.340 Ligands: GOL.30, U5C.39 24 PLIP interactions: 24 interactions with chain C Hydrophobic interactions: C:T.188, C:V.220, C:N.340 Hydrogen bonds: C:R.73, C:D.145, C:G.147, C:R.184, 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:R.73, C:T.188, C:G.218, C:G.221, C:D.240, C:D.240 NAD.42: 22 residues within 4Å: Chain D: R.73, D.145, M.146, G.147, R.184, T.188, G.216, F.217, G.218, N.219, V.220, S.239, D.240, I.241, C.291, A.292, A.313, A.314, N.315, N.340 Ligands: GOL.43, U5C.47 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:T.188, D:V.220, D:N.340 Hydrogen bonds: D:R.73, D:D.145, D:G.147, D:R.184, D:R.184, 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:R.73, D:T.188, D:G.218, D:G.221 NAD.50: 22 residues within 4Å: Chain E: 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, C.291, A.292, A.313, A.314, N.315, N.340 Ligands: GOL.51, U5C.58 23 PLIP interactions: 23 interactions with chain E Hydrophobic interactions: E:T.188, E:V.220, E:N.340 Hydrogen bonds: E:R.73, E:D.145, E:G.147, E:R.184, E:R.184, E:F.217, E:F.217, E:N.219, E:N.219, E:V.220, E:I.241, E:A.292, E:N.315, E:N.315 Water bridges: E:R.73, E:T.188, E:G.218, E:G.221, E:D.240, E:D.240 NAD.60: 23 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, S.239, D.240, I.241, C.291, A.292, A.313, A.314, N.315, N.340 Ligands: GOL.61, U5C.65 24 PLIP interactions: 24 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: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:R.73, F:R.113, F:T.188, F:G.218, F:G.221, F:D.240, F:K.260

26 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: P.144, N.149, A.150, G.173, E.185, N.219 Ligands: NAD.1 Ligand excluded by PLIP GOL.3: 4 residues within 4Å: Chain A: Q.129, K.130 Chain D: K.162 Chain F: F.35 Ligand excluded by PLIP GOL.4: 5 residues within 4Å: Chain A: Q.356, W.360, K.364 Chain B: F.358 Ligands: GOL.34 Ligand excluded by PLIP GOL.6: 5 residues within 4Å: Chain A: R.65, D.98, R.402, R.405 Chain B: D.177 Ligand excluded by PLIP GOL.7: 6 residues within 4Å: Chain A: D.47, S.118 Chain D: D.47, D.48, G.49 Ligands: NA.11 Ligand excluded by PLIP GOL.9: 5 residues within 4Å: Chain A: E.41, T.43, K.130 Chain F: F.35, W.412 Ligand excluded by PLIP GOL.14: 7 residues within 4Å: Chain B: P.144, N.149, A.150, G.173, E.185, N.219 Ligands: NAD.12 Ligand excluded by PLIP GOL.17: 4 residues within 4Å: Chain B: P.112, G.147, T.148, N.149 Ligand excluded by PLIP GOL.18: 5 residues within 4Å: Chain B: R.65, D.98, R.402, R.405 Chain C: D.177 Ligand excluded by PLIP GOL.19: 6 residues within 4Å: Chain A: P.100, W.351 Chain B: P.168, N.354, G.357, M.359 Ligand excluded by PLIP GOL.21: 4 residues within 4Å: Chain B: L.199, Y.203, C.384, L.391 Ligand excluded by PLIP GOL.23: 6 residues within 4Å: Chain B: D.47, S.118 Chain F: D.47, D.48, G.49 Ligands: NA.27 Ligand excluded by PLIP GOL.24: 5 residues within 4Å: Chain B: D.47, D.48, G.49 Chain F: D.47 Ligands: NA.27 Ligand excluded by PLIP GOL.30: 6 residues within 4Å: Chain C: P.144, A.150, G.173, E.185, N.219 Ligands: NAD.28 Ligand excluded by PLIP GOL.34: 5 residues within 4Å: Chain A: F.358 Chain C: Q.356, W.360, K.364 Ligands: GOL.4 Ligand excluded by PLIP GOL.35: 6 residues within 4Å: Chain B: P.100, W.351 Chain C: P.168, N.354, G.357, M.359 Ligand excluded by PLIP GOL.37: 1 residues within 4Å: Chain C: Y.203 Ligand excluded by PLIP GOL.38: 5 residues within 4Å: Chain C: D.47, D.48 Chain E: D.47 Ligands: NA.41, GOL.49 Ligand excluded by PLIP GOL.43: 6 residues within 4Å: Chain D: P.144, N.149, A.150, G.173, N.219 Ligands: NAD.42 Ligand excluded by PLIP GOL.44: 5 residues within 4Å: Chain D: P.168, N.354, G.357, M.359 Chain F: P.100 Ligand excluded by PLIP GOL.46: 6 residues within 4Å: Chain A: D.47, D.48, G.49 Chain D: D.47, S.118 Ligands: NA.11 Ligand excluded by PLIP GOL.49: 6 residues within 4Å: Chain C: D.47 Chain E: D.47, D.48, G.49 Ligands: GOL.38, NA.41 Ligand excluded by PLIP GOL.51: 8 residues within 4Å: Chain E: P.144, T.148, N.149, A.150, G.173, E.185, N.219 Ligands: NAD.50 Ligand excluded by PLIP GOL.53: 5 residues within 4Å: Chain D: P.100 Chain E: P.168, N.354, G.357, M.359 Ligand excluded by PLIP GOL.55: 5 residues within 4Å: Chain E: Q.356, W.360, K.364 Chain F: Q.356, F.358 Ligand excluded by PLIP GOL.61: 7 residues within 4Å: Chain F: P.144, N.149, A.150, G.173, E.185, N.219 Ligands: NAD.60 Ligand excluded by PLIP

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

EDO.5: 4 residues within 4Å: Chain A: L.182, G.183, E.185, E.362 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.183, A:E.362 Water bridges: A:E.185, A:E.185, A:E.185 EDO.15: 4 residues within 4Å: Chain B: Q.356, W.360, K.364 Chain C: F.358 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Water bridges: C:Q.356, C:F.358 Hydrogen bonds: B:Q.356, B:K.364, B:K.364 EDO.16: 4 residues within 4Å: Chain B: T.222, W.223, K.226, I.257 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.222 Water bridges: B:K.226, B:N.254 EDO.20: 4 residues within 4Å: Chain B: L.182, G.183, E.185, E.362 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.183, B:E.185, B:E.362 Water bridges: B:E.185, B:E.185, B:E.185 EDO.32: 3 residues within 4Å: Chain C: T.222, W.223, K.226 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.222, C:W.223 Water bridges: C:K.226, C:K.226 EDO.33: 6 residues within 4Å: Chain A: D.177 Chain C: R.65, D.98, R.402, R.405, A.406 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.65, C:D.98, C:R.402, C:R.405, C:A.406 EDO.36: 4 residues within 4Å: Chain C: R.190, V.193, F.194, K.231 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.190 Water bridges: C:R.190 EDO.52: 4 residues within 4Å: Chain B: R.29 Chain E: Y.54, I.55, G.109 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain E Hydrogen bonds: B:R.29, E:I.55 Water bridges: E:G.109 EDO.54: 5 residues within 4Å: Chain E: R.65, D.98, R.402, R.405 Chain F: D.177 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.65, E:D.98, E:R.402 EDO.57: 3 residues within 4Å: Chain E: R.246, E.279, H.283 2 PLIP interactions: 2 interactions with chain E Water bridges: E:H.283, E:H.283 EDO.62: 6 residues within 4Å: Chain D: D.177 Chain F: R.65, D.98, R.402, R.405, A.406 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:R.65, F:D.98, F:R.402, F:A.406 EDO.64: 5 residues within 4Å: Chain D: Q.356, F.358 Chain F: Q.356, W.360, K.364 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain D Hydrogen bonds: F:Q.356, F:K.364, F:K.364, D:Q.356

6 x U5C: 2,2-bis(oxidanyl)pentanedioic acid(Non-covalent)

U5C.8: 15 residues within 4Å: Chain A: K.69, G.70, G.71, M.90, K.93, K.105, A.143, P.144, D.145, R.184, N.315, G.343, V.344, S.347 Ligands: NAD.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:A.143 Hydrogen bonds: A:G.71, A:K.105, A:D.145, A:T.172, A:N.315, A:S.347 Water bridges: A:K.93, A:K.93, A:N.340 Salt bridges: A:K.69, A:K.93, A:K.105, A:R.184 U5C.25: 15 residues within 4Å: Chain B: K.69, G.70, G.71, M.90, K.93, K.105, A.143, P.144, D.145, R.184, N.315, G.343, V.344, S.347 Ligands: NAD.12 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:A.143 Hydrogen bonds: B:G.71, B:K.105, B:D.145, B:N.315, B:S.347 Water bridges: B:K.93, B:K.93, B:N.340 Salt bridges: B:K.69, B:K.93, B:K.105, B:R.184 U5C.39: 15 residues within 4Å: Chain C: K.69, G.70, G.71, M.90, K.93, K.105, A.143, P.144, D.145, R.184, N.315, G.343, V.344, S.347 Ligands: NAD.28 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:A.143 Hydrogen bonds: C:G.71, C:K.105, C:D.145, C:N.315, C:S.347 Water bridges: C:K.93, C:N.340 Salt bridges: C:K.69, C:K.93, C:K.105, C:R.184 U5C.47: 15 residues within 4Å: Chain D: K.69, G.70, G.71, M.90, K.93, K.105, A.143, P.144, D.145, R.184, N.315, G.343, V.344, S.347 Ligands: NAD.42 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:A.143 Hydrogen bonds: D:G.71, D:K.105, D:D.145, D:T.172, D:N.315, D:S.347 Water bridges: D:K.93 Salt bridges: D:K.69, D:K.93, D:K.105, D:R.184 U5C.58: 15 residues within 4Å: Chain E: K.69, G.70, G.71, M.90, K.93, K.105, A.143, P.144, D.145, R.184, N.315, G.343, V.344, S.347 Ligands: NAD.50 12 PLIP interactions: 12 interactions with chain E Hydrophobic interactions: E:A.143 Hydrogen bonds: E:G.71, E:K.105, E:D.145, E:N.315, E:S.347 Water bridges: E:K.93, E:K.93 Salt bridges: E:K.69, E:K.93, E:K.105, E:R.184 U5C.65: 15 residues within 4Å: Chain F: K.69, G.70, G.71, M.90, K.93, K.105, A.143, P.144, D.145, R.184, N.315, G.343, V.344, S.347 Ligands: NAD.60 13 PLIP interactions: 13 interactions with chain F Hydrophobic interactions: F:A.143 Hydrogen bonds: F:G.71, F:K.105, F:D.145, F:T.172, F:N.315, F:S.347 Water bridges: F:K.93, F:K.93 Salt bridges: F:K.69, F:K.93, F:K.105, F:R.184

6 x CA: CALCIUM ION(Non-covalent)

CA.10: 3 residues within 4Å: Chain A: S.30, I.33 Chain F: E.41 6 PLIP interactions: 2 interactions with chain A, 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: A:S.30, A:I.33, F:E.41, H2O.4, H2O.4, H2O.77 CA.26: 3 residues within 4Å: Chain B: S.30, I.33 Chain E: E.41 6 PLIP interactions: 1 interactions with chain E, 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: E:E.41, B:S.30, B:I.33, H2O.17, H2O.20, H2O.64 CA.40: 3 residues within 4Å: Chain C: S.30, I.33 Chain D: E.41 6 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: C:S.30, C:I.33, D:E.41, H2O.31, H2O.33, H2O.51 CA.48: 3 residues within 4Å: Chain C: E.41 Chain D: S.30, I.33 6 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: D:S.30, D:I.33, C:E.41, H2O.38, H2O.45, H2O.46 CA.59: 3 residues within 4Å: Chain B: E.41 Chain E: S.30, I.33 6 PLIP interactions: 2 interactions with chain E, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: E:S.30, E:I.33, B:E.41, H2O.23, H2O.58, H2O.59 CA.66: 3 residues within 4Å: Chain A: E.41 Chain F: S.30, I.33 6 PLIP interactions: 2 interactions with chain F, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: F:S.30, F:I.33, A:E.41, H2O.8, H2O.70, H2O.72

3 x NA: SODIUM ION(Non-functional Binders)

NA.11: 4 residues within 4Å: Chain A: D.47 Chain D: D.47 Ligands: GOL.7, GOL.46 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.47 NA.27: 4 residues within 4Å: Chain B: D.47 Chain F: D.47 Ligands: GOL.23, GOL.24 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:D.47 NA.41: 4 residues within 4Å: Chain C: D.47 Chain E: D.47 Ligands: GOL.38, GOL.49 No protein-ligand interaction detected (PLIP)

7 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.13: 6 residues within 4Å: Chain B: N.5, L.7, A.8, N.11, R.15, D.81 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.11, B:R.15, B:R.15 PEG.22: 4 residues within 4Å: Chain B: R.190, F.194, K.231, N.366 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.190 Water bridges: B:R.190, B:N.366 PEG.29: 6 residues within 4Å: Chain C: N.5, L.7, A.8, N.11, R.15, D.81 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.11, C:R.15, C:R.15, C:D.81 PEG.31: 6 residues within 4Å: Chain C: D.268, F.269, N.270, G.272, D.273, A.274 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.268, C:A.274 Water bridges: C:D.268, C:D.268, C:D.268 PEG.45: 5 residues within 4Å: Chain D: Q.356, W.360, K.364, E.368 Chain E: F.358 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:Q.356, D:K.364, E:Q.356 PEG.56: 5 residues within 4Å: Chain E: R.190, V.193, F.194, K.231, N.366 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:R.190, E:N.366 Water bridges: E:N.366, E:N.366 PEG.63: 5 residues within 4Å: Chain F: N.5, A.8, N.11, R.15, D.81 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:N.11, F:R.15, F:D.81 Water bridges: F:R.15

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grzechowiak, M. et al., Structural and functional studies of Arabidopsis thaliana glutamate dehydrogenase isoform 2 demonstrate enzyme dynamics and identify its calcium binding site. Plant Physiol Biochem. (2023)

Release Date

2023-08-09

Peptides

Glutamate dehydrogenase 2: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Glutamate dehydrogenase 2

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