SMTL ID : 5gud.1

Glutamate dehydrogenase from Corynebacterium glutamicum (alpha-iminoglutarate/NADP+ complex)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

homo-hexamer

Ligands

4 x 2IT: (2Z)-2-iminopentanedioic acid(Non-covalent)

2IT.1: 14 residues within 4Å: Chain A: K.116, G.117, G.118, Q.137, K.140, K.152, A.190, G.191, D.192, R.232, N.371, V.400, S.403 Ligands: NDP.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:A.190 Hydrogen bonds: A:Q.137, A:K.152, A:D.192, A:D.192, A:T.220, A:N.371, A:G.399, A:S.403 Water bridges: A:K.140, A:N.396 Salt bridges: A:K.116, A:K.140, A:K.152, A:R.232 2IT.6: 16 residues within 4Å: Chain B: K.116, G.117, G.118, Q.137, K.140, K.152, A.190, G.191, D.192, T.220, R.232, N.371, G.399, V.400, S.403 Ligands: NDP.7 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:Q.137, B:K.152, B:D.192, B:D.192, B:T.220, B:N.371, B:S.403 Water bridges: B:K.140 Salt bridges: B:K.116, B:K.140, B:K.152, B:R.232 2IT.9: 14 residues within 4Å: Chain C: K.116, G.117, G.118, Q.137, K.140, K.152, A.190, G.191, D.192, R.232, N.371, V.400, S.403 Ligands: NDP.10 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:Q.137, C:K.152, C:D.192, C:D.192, C:T.220, C:N.371, C:G.399, C:S.403 Water bridges: C:K.140, C:K.140 Salt bridges: C:K.116, C:K.140, C:K.152, C:R.232 2IT.22: 14 residues within 4Å: Chain F: K.116, G.117, G.118, Q.137, K.140, K.152, A.190, G.191, D.192, R.232, N.371, V.400, S.403 Ligands: NDP.23 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:Q.137, F:K.152, F:D.192, F:D.192, F:N.371, F:S.403 Water bridges: F:K.140, F:N.396 Salt bridges: F:K.116, F:K.140, F:K.152, F:R.232

6 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.2: 25 residues within 4Å: Chain A: R.120, H.122, K.160, D.192, I.193, G.194, R.232, T.236, G.264, S.265, G.266, N.267, V.268, S.287, D.288, S.289, R.314, C.344, A.345, T.346, G.369, A.370, N.371, N.396 Ligands: 2IT.1 32 PLIP interactions: 32 interactions with chain A Hydrophobic interactions: A:T.236, A:V.268, A:N.396 Hydrogen bonds: A:R.120, A:H.122, A:D.192, A:G.194, A:R.232, A:R.232, A:T.236, A:S.265, A:N.267, A:N.267, A:V.268, A:S.289, A:A.345, A:N.371, A:N.371 Water bridges: A:R.120, A:S.124, A:K.160, A:D.192, A:T.236, A:G.266, A:A.269, A:R.314, A:T.346, A:Q.347 Salt bridges: A:K.160, A:K.308, A:R.314 pi-Cation interactions: A:K.152 NDP.7: 25 residues within 4Å: Chain B: R.120, H.122, K.160, D.192, I.193, G.194, R.232, T.236, G.264, S.265, G.266, N.267, V.268, S.287, D.288, S.289, R.314, C.344, A.345, T.346, G.369, A.370, N.371, N.396 Ligands: 2IT.6 32 PLIP interactions: 32 interactions with chain B Hydrophobic interactions: B:T.236, B:V.268, B:N.396 Hydrogen bonds: B:R.120, B:H.122, B:D.192, B:G.194, B:R.232, B:R.232, B:S.265, B:N.267, B:N.267, B:V.268, B:S.289, B:S.289, B:A.345, B:N.371, B:N.371 Water bridges: B:R.120, B:S.124, B:K.160, B:D.192, B:T.236, B:G.266, B:G.266, B:K.308, B:R.314, B:Q.347 Salt bridges: B:K.160, B:K.308, B:R.314 pi-Cation interactions: B:K.152 NDP.10: 24 residues within 4Å: Chain C: R.120, K.140, K.160, D.192, I.193, G.194, R.232, T.236, S.265, G.266, N.267, V.268, S.287, D.288, S.289, R.314, C.344, A.345, T.346, G.369, A.370, N.371, N.396 Ligands: 2IT.9 31 PLIP interactions: 31 interactions with chain C Hydrophobic interactions: C:T.236, C:V.268, C:N.396 Hydrogen bonds: C:R.120, C:D.192, C:G.194, C:R.232, C:R.232, C:T.236, C:S.265, C:N.267, C:N.267, C:V.268, C:S.289, C:S.289, C:A.345, C:N.371, C:N.371 Water bridges: C:H.122, C:K.160, C:D.192, C:G.266, C:A.269, C:S.287, C:R.314, C:T.346, C:Q.347 Salt bridges: C:K.160, C:K.308, C:R.314 pi-Cation interactions: C:K.152 NDP.14: 14 residues within 4Å: Chain D: T.236, S.265, G.266, N.267, V.268, S.287, D.288, S.289, R.314, C.344, A.345, T.346, A.370, N.371 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:S.265, D:N.267, D:N.267, D:V.268, D:S.289, D:S.289, D:A.345, D:Q.347, D:N.371 Water bridges: D:T.236, D:G.266, D:A.269, D:T.346, D:T.346, D:N.371 Salt bridges: D:K.308, D:R.314 NDP.18: 17 residues within 4Å: Chain E: T.236, G.264, S.265, G.266, N.267, V.268, S.287, D.288, S.289, R.314, C.344, A.345, T.346, G.369, A.370, N.371 Ligands: CIT.17 21 PLIP interactions: 21 interactions with chain E Hydrogen bonds: E:T.236, E:S.265, E:N.267, E:N.267, E:V.268, E:S.289, E:S.289, E:A.345, E:Q.347, E:N.371 Water bridges: E:T.236, E:G.266, E:A.269, E:S.287, E:S.289, E:S.289, E:S.289, E:K.308, E:R.314 Salt bridges: E:K.308, E:R.314 NDP.23: 25 residues within 4Å: Chain F: R.120, H.122, K.160, D.192, I.193, G.194, R.232, T.236, G.264, S.265, G.266, N.267, V.268, S.287, D.288, S.289, R.314, C.344, A.345, T.346, G.369, A.370, N.371, N.396 Ligands: 2IT.22 34 PLIP interactions: 34 interactions with chain F Hydrophobic interactions: F:T.236, F:V.268 Hydrogen bonds: F:R.120, F:D.192, F:G.194, F:R.232, F:R.232, F:S.265, F:N.267, F:N.267, F:V.268, F:S.289, F:S.289, F:S.289, F:A.345, F:T.346, F:N.371, F:N.371 Water bridges: F:R.120, F:S.124, F:K.160, F:K.160, F:K.160, F:D.192, F:T.236, F:G.266, F:A.269, F:K.308, F:R.314, F:T.346 Salt bridges: F:K.160, F:K.308, F:R.314 pi-Cation interactions: F:K.152

14 x K: POTASSIUM ION(Non-covalent)

K.3: 3 residues within 4Å: Chain A: A.319, I.322, A.325 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.319, A:I.322, A:A.325, H2O.2, H2O.14 K.4: 3 residues within 4Å: Chain A: H.179, I.182, Y.207 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.179, A:I.182, A:Y.207, H2O.13, H2O.18 K.5: 3 residues within 4Å: Chain A: S.254, S.256, Q.258 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.254, A:S.256, H2O.14, H2O.17 K.8: 3 residues within 4Å: Chain B: H.179, I.182, Y.207 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.179, B:I.182, B:Y.207, H2O.33, H2O.33 K.11: 3 residues within 4Å: Chain C: H.179, I.182, Y.207 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.179, C:I.182, C:Y.207, H2O.46, H2O.49 K.12: 3 residues within 4Å: Chain C: S.254, S.256, Q.258 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:S.254, C:S.256, H2O.40 K.13: 3 residues within 4Å: Chain B: A.411 Chain D: A.411 Chain F: A.411 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: D:A.411, F:A.411, H2O.28, H2O.60, H2O.99 K.15: 3 residues within 4Å: Chain D: H.179, I.182, Y.207 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.179, D:I.182, D:Y.207, H2O.63, H2O.64 K.16: 3 residues within 4Å: Chain A: A.411 Chain C: A.411 Chain E: A.411 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: C:A.411, E:A.411, H2O.11, H2O.41, H2O.77 K.19: 3 residues within 4Å: Chain E: S.254, S.256, Q.258 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:S.254, E:S.254, E:S.256, H2O.79, H2O.84 K.20: 3 residues within 4Å: Chain E: H.179, I.182, Y.207 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:H.179, E:I.182, E:Y.207, H2O.84, H2O.84 K.21: 4 residues within 4Å: Chain E: A.319, I.322, G.324, A.325 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:A.319, E:I.322, E:A.325 K.24: 3 residues within 4Å: Chain F: H.179, I.182, Y.207 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.179, F:I.182, F:Y.207, H2O.103 K.25: 3 residues within 4Å: Chain F: A.319, I.322, A.325 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:A.319, F:I.322, F:A.325

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.17: 12 residues within 4Å: Chain E: G.117, G.118, Q.137, K.140, K.152, A.190, G.191, D.192, T.220, V.400, S.403 Ligands: NDP.18 14 PLIP interactions: 14 interactions with chain E Hydrophobic interactions: E:V.400 Hydrogen bonds: E:G.118, E:Q.137, E:T.220, E:S.403 Water bridges: E:K.140, E:G.191, E:T.236, E:T.236, E:G.399, E:V.400 Salt bridges: E:K.116, E:K.140, E:K.152

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tomita, T. et al., Crystal structure of the 2-iminoglutarate-bound complex of glutamate dehydrogenase from Corynebacterium glutamicum. FEBS Lett. (2017)

Release Date

2017-06-07

Peptides

Glutamate dehydrogenase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Glutamate dehydrogenase