SMTL ID : 8ar7.1

Bovine glutamate dehydrogenase in ternary complex with the allosteric activators ADP and leucine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-hexamer

Ligands

6 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 15 residues within 4Å: Chain A: H.145, R.146, C.175, A.176, D.179, V.180, F.182, R.519, K.548, V.552 Chain B: I.263, H.269, K.447, S.453, R.456 14 PLIP interactions: 9 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:R.146, A:D.179, A:V.180, A:F.182, B:S.453 Water bridges: A:Q.523, B:S.453 Salt bridges: A:R.519, B:H.269, B:K.447, B:R.456 pi-Cation interactions: A:R.146, A:R.146, A:K.548 ADP.5: 16 residues within 4Å: Chain B: H.145, R.146, C.175, A.176, D.179, V.180, P.181, F.182, R.519, K.548, V.552 Chain C: I.263, H.269, K.447, S.453, R.456 13 PLIP interactions: 8 interactions with chain B, 5 interactions with chain C Hydrogen bonds: B:R.146, B:D.179, B:V.180, B:F.182, C:S.453 Salt bridges: B:R.519, C:H.269, C:K.447, C:R.456 pi-Cation interactions: B:R.146, B:R.146, B:K.548 Water bridges: C:R.456 ADP.8: 16 residues within 4Å: Chain A: I.263, H.269, K.447, S.453, R.456 Chain C: H.145, R.146, C.175, A.176, D.179, V.180, P.181, F.182, R.519, K.548, V.552 18 PLIP interactions: 12 interactions with chain C, 6 interactions with chain A Hydrogen bonds: C:R.146, C:D.179, C:V.180, C:F.182, A:S.453 Water bridges: C:A.176, C:A.176, C:D.179, C:Q.523, A:S.453, A:S.453 Salt bridges: C:R.519, A:H.269, A:K.447, A:R.456 pi-Cation interactions: C:R.146, C:R.146, C:K.548 ADP.12: 15 residues within 4Å: Chain D: H.145, R.146, C.175, A.176, D.179, V.180, F.182, R.519, K.548, V.552 Chain E: I.263, H.269, K.447, S.453, R.456 19 PLIP interactions: 13 interactions with chain D, 6 interactions with chain E Hydrogen bonds: D:R.146, D:D.179, D:V.180, D:F.182, E:S.453 Water bridges: D:A.176, D:A.176, D:D.179, D:R.519, D:Q.523, E:R.456, E:R.456 Salt bridges: D:R.519, E:H.269, E:K.447, E:R.456 pi-Cation interactions: D:R.146, D:R.146, D:K.548 ADP.15: 16 residues within 4Å: Chain E: H.145, R.146, C.175, A.176, D.179, V.180, P.181, F.182, R.519, K.548, V.552 Chain F: I.263, H.269, K.447, S.453, R.456 18 PLIP interactions: 9 interactions with chain E, 9 interactions with chain F Hydrogen bonds: E:R.146, E:V.180, E:F.182, F:S.453 Water bridges: E:A.176, E:A.176, F:H.269, F:S.453, F:R.456, F:R.456, F:E.505 Salt bridges: E:R.519, F:H.269, F:K.447, F:R.456 pi-Cation interactions: E:R.146, E:R.146, E:K.548 ADP.17: 15 residues within 4Å: Chain D: I.263, H.269, K.447, S.453, R.456 Chain F: H.145, R.146, C.175, A.176, D.179, V.180, F.182, R.519, K.548, V.552 21 PLIP interactions: 13 interactions with chain F, 8 interactions with chain D Hydrogen bonds: F:R.146, F:D.179, F:V.180, F:F.182, D:S.453 Water bridges: F:A.176, F:A.176, F:D.179, F:R.519, F:Q.523, D:H.269, D:S.453, D:R.456, D:R.456 Salt bridges: F:R.519, D:H.269, D:K.447, D:R.456 pi-Cation interactions: F:R.146, F:R.146, F:K.548

6 x K: POTASSIUM ION(Non-covalent)

K.2: 5 residues within 4Å: Chain A: I.111, I.112, P.114, N.116, H.142 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:I.111, A:P.114, A:H.142, H2O.1 K.6: 5 residues within 4Å: Chain B: I.111, I.112, P.114, N.116, H.142 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:I.111, B:I.112, B:P.114, B:H.142, H2O.4 K.9: 5 residues within 4Å: Chain C: I.111, I.112, P.114, N.116, H.142 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:I.111, C:I.112, C:P.114, C:H.142, H2O.6 K.13: 5 residues within 4Å: Chain D: I.111, I.112, P.114, N.116, H.142 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:P.114, D:H.142, H2O.9 K.16: 5 residues within 4Å: Chain E: I.111, I.112, P.114, N.116, H.142 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:I.111, E:I.112, E:P.114, E:H.142, H2O.12 K.18: 6 residues within 4Å: Chain F: I.111, I.112, P.114, N.116, H.142, S.143 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:I.111, F:P.114, F:H.142

6 x LEU: LEUCINE(Non-covalent)

LEU.3: 10 residues within 4Å: Chain A: D.241 Chain C: Q.144, H.145, V.552, Y.553, A.556, G.557, V.558, T.559 Chain F: R.207 9 PLIP interactions: 1 interactions with chain A, 1 interactions with chain F, 5 interactions with chain C, 2 Ligand-Ligand interactions Hydrogen bonds: A:D.241, C:T.559, C:T.559, L.3, L.3 Salt bridges: F:R.207 Hydrophobic interactions: C:V.552, C:Y.553, C:A.556 LEU.4: 10 residues within 4Å: Chain A: R.207 Chain E: Q.144, H.145, V.552, Y.553, A.556, G.557, V.558, T.559 Chain F: D.241 9 PLIP interactions: 7 interactions with chain E, 1 interactions with chain F, 1 interactions with chain A Hydrophobic interactions: E:V.552, E:Y.553, E:A.556 Hydrogen bonds: E:T.559, F:D.241 Water bridges: E:Q.144, E:Y.553, E:Y.553 Salt bridges: A:R.207 LEU.7: 10 residues within 4Å: Chain B: R.207 Chain D: Q.144, H.145, V.552, Y.553, A.556, G.557, V.558, T.559 Chain E: D.241 7 PLIP interactions: 1 interactions with chain B, 1 interactions with chain E, 5 interactions with chain D, Salt bridges: B:R.207 Hydrogen bonds: E:D.241, D:T.559 Hydrophobic interactions: D:V.552, D:Y.553, D:A.556 Water bridges: D:Y.553 LEU.10: 10 residues within 4Å: Chain C: R.207 Chain D: D.241 Chain F: Q.144, H.145, V.552, Y.553, A.556, G.557, V.558, T.559 7 PLIP interactions: 6 interactions with chain F, 1 interactions with chain C, Hydrophobic interactions: F:H.145, F:V.552, F:Y.553, F:A.556 Hydrogen bonds: F:T.559, F:T.559 Salt bridges: C:R.207 LEU.11: 10 residues within 4Å: Chain B: Q.144, H.145, V.552, Y.553, A.556, G.557, V.558, T.559 Chain C: D.241 Chain D: R.207 9 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C, 2 Ligand-Ligand interactions, 1 interactions with chain D Hydrophobic interactions: B:V.552, B:Y.553, B:A.556 Hydrogen bonds: B:T.559, B:T.559, C:D.241, L.11, L.11 Salt bridges: D:R.207 LEU.14: 10 residues within 4Å: Chain A: Q.144, H.145, V.552, Y.553, A.556, G.557, V.558, T.559 Chain B: D.241 Chain E: R.207 11 PLIP interactions: 1 interactions with chain B, 1 interactions with chain E, 7 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: B:D.241, A:T.559, A:T.559, L.14, L.14 Salt bridges: E:R.207 Hydrophobic interactions: A:V.552, A:Y.553, A:A.556 Water bridges: A:N.116, A:N.116

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Aleshin, V.A. et al., Structural Basis for the Binding of Allosteric Activators Leucine and ADP to Mammalian Glutamate Dehydrogenase. Int J Mol Sci (2022)

Release Date

2022-10-05

Peptides

Glutamate dehydrogenase (NAD(P)(+)): ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Glutamate dehydrogenase (NAD(P)(+))

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