SMTL ID : 3blw.2 (5 other biounits)

Yeast Isocitrate Dehydrogenase with Citrate and AMP Bound in the Regulatory Subunits

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 4.30 Å

Oligo State

hetero-4-4-mer

Ligands

4 x FLC: CITRATE ANION(Non-covalent)

FLC.1: 11 residues within 4Å: Chain A: T.83, S.92, N.94, V.95, R.98, R.129, F.136, T.241, R.274 Chain B: K.189, T.191 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.95, A:F.136 Hydrogen bonds: A:T.83, A:S.92, A:N.94 Salt bridges: A:R.98, A:R.129, A:R.129, A:R.274, A:R.274, B:K.189 FLC.3: 11 residues within 4Å: Chain C: T.83, S.92, N.94, R.98, R.129, F.136, T.241, R.274 Chain D: K.189, T.191, D.222 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:T.83, C:S.92, C:N.94 Salt bridges: C:R.98, C:R.129, C:R.129, C:R.274, C:R.274, D:K.189 FLC.5: 10 residues within 4Å: Chain E: T.83, S.92, N.94, V.95, R.98, R.129, F.136, T.241, R.274 Chain F: K.189 11 PLIP interactions: 10 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:N.94 Hydrogen bonds: E:T.83, E:S.92, E:N.94, E:T.241 Salt bridges: E:R.98, E:R.129, E:R.129, E:R.274, E:R.274, F:K.189 FLC.7: 10 residues within 4Å: Chain G: T.83, S.92, N.94, V.95, R.98, R.129, F.136, T.241, R.274 Chain H: K.189 10 PLIP interactions: 9 interactions with chain G, 1 interactions with chain H Hydrophobic interactions: G:V.95, G:F.136 Hydrogen bonds: G:S.92, G:N.94 Salt bridges: G:R.98, G:R.129, G:R.129, G:R.274, G:R.274, H:K.189

4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 8 residues within 4Å: Chain A: V.28, H.275, G.277, D.279, A.286, N.287, D.328 Chain B: N.223 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.277, A:N.287, A:N.287, B:N.223, B:N.223, B:N.223 Salt bridges: A:H.275 AMP.4: 8 residues within 4Å: Chain C: V.28, H.275, V.276, G.277, D.279, A.286, N.287 Chain D: N.223 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:V.276, C:G.277, C:N.287, D:N.223 AMP.6: 9 residues within 4Å: Chain E: I.32, G.255, H.275, V.276, G.277, D.279, N.287, D.328 Chain F: N.223 7 PLIP interactions: 6 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:V.276, E:G.277, E:L.278, E:D.279, E:N.287, F:N.223 Salt bridges: E:H.275 AMP.8: 9 residues within 4Å: Chain G: V.28, I.32, H.275, V.276, G.277, D.279, N.287, D.328 Chain H: N.223 7 PLIP interactions: 6 interactions with chain G, 1 interactions with chain H Hydrogen bonds: G:V.276, G:G.277, G:D.279, G:N.287, G:N.287, H:N.223 Salt bridges: G:H.275

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Taylor, A.B. et al., Allosteric Motions in Structures of Yeast NAD+-specific Isocitrate Dehydrogenase. J.Biol.Chem. (2008)

Release Date

2008-02-05

Peptides

Isocitrate dehydrogenase [NAD] subunit 1: ACEG
Isocitrate dehydrogenase [NAD] subunit 2: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
I

C
K

E
M

G
O

B
J

D
L

F
N

H
P

Isocitrate dehydrogenase [NAD] subunit 1

Isocitrate dehydrogenase [NAD] subunit 2

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