SMTL ID : 1nqt.3 (2 other biounits)

Crystal structure of bovine Glutamate dehydrogenase-ADP complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

homo-12-mer

Ligands

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

ADP.1: 17 residues within 4Å: Chain A: Q.80, R.81, C.110, A.111, D.114, V.115, P.116, F.117, R.454, K.483, V.484, V.487 Chain B: I.198, H.204, K.382, S.388, R.391 12 PLIP interactions: 4 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:S.388, A:R.81, A:D.114, A:D.114, A:V.115 Salt bridges: B:H.204, B:K.382, B:R.391, A:R.454 pi-Cation interactions: A:R.81, A:R.81, A:K.483 ADP.2: 15 residues within 4Å: Chain B: Q.80, R.81, A.111, D.114, V.115, R.454, K.483, V.484, V.487 Chain F: I.198, H.204, K.382, S.388, R.391, E.440 13 PLIP interactions: 8 interactions with chain B, 5 interactions with chain F Hydrogen bonds: B:R.81, B:D.114, B:D.114, B:V.115, F:S.388, F:E.440 Salt bridges: B:R.454, F:H.204, F:K.382, F:R.391 pi-Cation interactions: B:R.81, B:R.81, B:K.483 ADP.3: 15 residues within 4Å: Chain C: Q.80, R.81, A.111, D.114, V.115, R.454, K.483, V.484, V.487 Chain D: I.198, H.204, K.382, S.388, R.391, E.440 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:R.81, C:D.114, C:V.115 Salt bridges: C:R.454, D:H.204, D:K.382, D:R.391 pi-Cation interactions: C:R.81, C:R.81 ADP.4: 14 residues within 4Å: Chain D: Q.80, R.81, C.110, A.111, D.114, V.115, R.454, V.487 Chain E: I.198, H.204, K.382, S.388, R.391, E.440 8 PLIP interactions: 5 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:S.388, E:E.440, D:C.110, D:D.114 Salt bridges: E:H.204, E:K.382, E:R.391, D:R.454 ADP.5: 15 residues within 4Å: Chain C: I.198, H.204, K.382, S.388, R.391, E.440 Chain E: Q.80, R.81, A.111, D.114, V.115, R.454, K.483, V.484, V.487 11 PLIP interactions: 6 interactions with chain E, 5 interactions with chain C Hydrogen bonds: E:D.114, E:V.115, E:R.454, C:S.388, C:E.440 pi-Cation interactions: E:R.81, E:R.81, E:K.483 Salt bridges: C:H.204, C:K.382, C:R.391 ADP.6: 14 residues within 4Å: Chain A: I.198, H.204, K.382, S.388, R.391 Chain F: Q.80, R.81, A.111, D.114, V.115, R.454, K.483, V.484, V.487 12 PLIP interactions: 5 interactions with chain A, 7 interactions with chain F Hydrogen bonds: A:S.388, A:S.388, F:R.81, F:D.114, F:D.114, F:V.115 Salt bridges: A:H.204, A:K.382, A:R.391, F:R.454 pi-Cation interactions: F:R.81, F:R.81 ADP.7: 15 residues within 4Å: Chain G: Q.80, R.81, A.111, D.114, V.115, R.454, K.483, V.484, V.487 Chain H: I.198, H.204, K.382, S.388, R.391, E.440 11 PLIP interactions: 6 interactions with chain G, 5 interactions with chain H Hydrogen bonds: G:R.81, G:D.114, G:V.115, H:S.388, H:E.440 Salt bridges: G:R.454, H:H.204, H:K.382, H:R.391 pi-Cation interactions: G:R.81, G:R.81 ADP.8: 14 residues within 4Å: Chain H: Q.80, R.81, A.111, D.114, V.115, R.454, K.483, V.484, V.487 Chain L: I.198, H.204, K.382, S.388, R.391 10 PLIP interactions: 7 interactions with chain H, 3 interactions with chain L Hydrogen bonds: H:D.114, H:D.114, H:V.115 Salt bridges: H:R.454, L:H.204, L:K.382, L:R.391 pi-Cation interactions: H:R.81, H:R.81, H:K.483 ADP.9: 14 residues within 4Å: Chain I: Q.80, R.81, A.111, D.114, V.115, R.454, K.483, V.484, V.487 Chain J: I.198, H.204, K.382, S.388, R.391 11 PLIP interactions: 4 interactions with chain J, 7 interactions with chain I Hydrogen bonds: J:S.388, I:R.81, I:D.114, I:D.114, I:V.115 Salt bridges: J:H.204, J:K.382, J:R.391, I:R.454 pi-Cation interactions: I:R.81, I:R.81 ADP.10: 15 residues within 4Å: Chain J: Q.80, R.81, A.111, D.114, V.115, F.117, R.454, K.483, V.484, V.487 Chain K: I.198, H.204, K.382, S.388, R.391 13 PLIP interactions: 4 interactions with chain K, 9 interactions with chain J Hydrogen bonds: K:S.388, J:R.81, J:D.114, J:D.114, J:D.114, J:V.115 Salt bridges: K:H.204, K:K.382, K:R.391, J:R.454 pi-Cation interactions: J:R.81, J:R.81, J:K.483 ADP.11: 16 residues within 4Å: Chain I: I.198, H.204, K.382, S.388, R.391 Chain K: Q.80, R.81, A.111, D.114, V.115, P.116, F.117, R.454, K.483, V.484, V.487 12 PLIP interactions: 8 interactions with chain K, 4 interactions with chain I Hydrogen bonds: K:D.114, K:D.114, K:D.114, K:V.115, I:S.388 Salt bridges: K:R.454, I:H.204, I:K.382, I:R.391 pi-Cation interactions: K:R.81, K:R.81, K:K.483 ADP.12: 16 residues within 4Å: Chain G: I.198, H.204, K.382, S.388, R.391 Chain L: Q.80, R.81, A.111, D.114, V.115, P.116, F.117, R.454, K.483, V.484, V.487 11 PLIP interactions: 6 interactions with chain L, 5 interactions with chain G Hydrogen bonds: L:R.81, L:D.114, L:V.115, G:S.388, G:E.440 Salt bridges: L:R.454, G:H.204, G:K.382, G:R.391 pi-Cation interactions: L:R.81, L:R.81

Links

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Citation

Banerjee, S. et al., Structural studies on ADP activation of mammalian glutamate dehydrogenase and the evolution of regulation. Biochemistry (2003)

Release Date

2003-05-06

Peptides

Glutamate dehydrogenase 1: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

Glutamate dehydrogenase 1

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