SMTL ID : 6yeh.1

Arabidopsis thaliana glutamate dehydrogenase isoform 1 in apo form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

homo-hexamer

Ligands

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

MPD.1: 6 residues within 4Å: Chain A: Y.74, L.120, G.147, G.149, T.152, W.155 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.74, A:L.120 MPD.2: 7 residues within 4Å: Chain A: L.199, 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, A:L.391 MPD.3: 10 residues within 4Å: Chain A: Y.166, P.168, G.179, Q.353, N.354, G.357, M.359 Chain E: P.67, P.100, W.351 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:N.354 Hydrophobic interactions: E:W.351 MPD.4: 5 residues within 4Å: Chain A: E.37, K.39, F.57, P.80 Chain B: K.39 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:K.39, A:F.57, A:P.80, B:K.39 MPD.7: 8 residues within 4Å: Chain B: E.37, I.38, K.39, F.57, V.59, V.78, P.80, V.83 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:K.39, B:F.57, B:F.57, B:V.78, B:V.83 Hydrogen bonds: B:E.37, B:E.37 MPD.9: 5 residues within 4Å: Chain C: E.37, F.57, V.78, P.80, V.83 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.57, C:F.57, C:V.78, C:V.83 MPD.10: 6 residues within 4Å: Chain C: Y.74, L.120, G.147, Q.151, T.152, W.155 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.74, C:L.120, C:Q.151 Hydrogen bonds: C:T.152 MPD.12: 7 residues within 4Å: Chain D: L.86, L.89, M.90, K.93, K.105, N.315, H.316 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.93, D:N.315 MPD.13: 4 residues within 4Å: Chain A: E.361 Chain E: D.367, E.368, T.371 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:T.371 Hydrogen bonds: E:D.367 MPD.15: 9 residues within 4Å: Chain C: P.67, P.100, W.351 Chain E: Y.166, P.168, G.179, Q.353, N.354, M.359 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain C Hydrophobic interactions: E:Y.166, E:P.168, C:P.100, C:W.351 Hydrogen bonds: E:N.354, E:N.354 MPD.16: 6 residues within 4Å: Chain E: E.37, I.38, K.39, F.57, V.59, P.80 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:K.39, E:K.39, E:V.59 Hydrogen bonds: E:E.37

6 x K: POTASSIUM ION(Non-covalent)

K.5: 4 residues within 4Å: Chain A: S.30, I.33, D.62 Chain B: E.41 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Metal complexes: B:E.41, A:S.30, A:I.33 K.6: 4 residues within 4Å: Chain A: E.41 Chain B: S.30, I.33, D.62 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Metal complexes: B:S.30, B:I.33, A:E.41 K.8: 4 residues within 4Å: Chain C: S.30, I.33, H.61 Chain D: E.41 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Metal complexes: D:E.41, C:S.30, C:I.33 K.11: 4 residues within 4Å: Chain C: E.41 Chain D: S.30, I.33, D.62 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Metal complexes: D:S.30, D:I.33, C:E.41 K.14: 4 residues within 4Å: Chain E: S.30, I.33, D.62 Chain F: E.41 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F Metal complexes: E:S.30, E:I.33, F:E.41 K.17: 5 residues within 4Å: Chain E: E.41 Chain F: S.30, I.33, H.61, D.62 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain E Metal complexes: F:S.30, F:I.33, E:E.41

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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