SMTL ID : 8ar8.1

Bovine glutamate dehydrogenase in complex with ADP at 2.4 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 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 20 PLIP interactions: 12 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:R.146, A:D.179, A:V.180, A:F.182, B:S.453 Water bridges: A:A.176, A:A.176, A:D.179, A:Q.523, B:S.453, B:S.453, B:R.456, B:R.456 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.2: 15 residues within 4Å: Chain B: H.145, R.146, C.175, A.176, D.179, V.180, F.182, R.519, K.548, V.552 Chain C: I.263, H.269, K.447, S.453, R.456 22 PLIP interactions: 11 interactions with chain B, 11 interactions with chain C Hydrogen bonds: B:R.146, B:D.179, B:V.180, B:F.182, C:S.453 Water bridges: B:D.179, B:R.519, B:Q.523, C:H.269, C:K.447, C:K.447, C:S.453, C:S.453, C:R.456, C:R.456 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 ADP.3: 16 residues within 4Å: Chain A: I.263, H.269, K.447, S.453, R.456, E.505 Chain C: H.145, R.146, C.175, A.176, D.179, V.180, F.182, R.519, K.548, V.552 22 PLIP interactions: 8 interactions with chain A, 14 interactions with chain C Hydrogen bonds: A:S.453, C:R.146, C:D.179, C:V.180, C:F.182 Water bridges: A:S.453, A:S.453, A:R.456, A:R.456, C:A.176, C:A.176, C:D.179, C:R.519, C:R.519, C:Q.523 Salt bridges: A:H.269, A:K.447, A:R.456, C:R.519 pi-Cation interactions: C:R.146, C:R.146, C:K.548 ADP.4: 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: 11 interactions with chain D, 8 interactions with chain E Hydrogen bonds: D:R.146, D:V.180, D:F.182, E:S.453, E:E.505 Water bridges: D:A.176, D:A.176, D:D.179, D:Q.523, E:S.453, E:R.456, E:R.456, E:R.456 Salt bridges: D:R.519, E:K.447, E:R.456 pi-Cation interactions: D:R.146, D:R.146, D:K.548 ADP.5: 15 residues within 4Å: Chain E: H.145, R.146, C.175, A.176, D.179, V.180, F.182, R.519, K.548, V.552 Chain F: I.263, H.269, K.447, S.453, R.456 19 PLIP interactions: 9 interactions with chain E, 10 interactions with chain F Hydrogen bonds: E:R.146, E:V.180, E:F.182, F:S.453, F:E.505 Water bridges: E:D.179, E:Q.523, F:H.269, F:S.453, F:R.456, F:R.456, F:R.456 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.6: 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 19 PLIP interactions: 9 interactions with chain F, 10 interactions with chain D Hydrogen bonds: F:R.146, F:V.180, F:F.182, D:S.453 Water bridges: F:D.179, F:Q.523, D:S.264, D:H.269, D:S.453, D:R.456, 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

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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