SMTL ID : 1lth.1 (1 other biounit)

T AND R STATES IN THE CRYSTALS OF BACTERIAL L-LACTATE DEHYDROGENASE REVEAL THE MECHANISM FOR ALLOSTERIC CONTROL

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 x FBP: 1,6-di-O-phosphono-beta-D-fructofuranose(Non-covalent)

FBP.1: 12 residues within 4Å: Chain A: R.158, K.170, N.171, H.173, Y.175, I.258 Chain D: R.158, K.170, N.171, H.173, Y.175 Ligands: FBP.7 14 PLIP interactions: 8 interactions with chain A, 6 interactions with chain D Hydrogen bonds: A:R.158, A:K.170, A:N.171, A:Y.175, A:Y.175, D:K.170, D:K.170, D:N.171 Salt bridges: A:R.158, A:H.173, A:H.173, D:R.158, D:H.173, D:H.173 FBP.3: 12 residues within 4Å: Chain B: R.158, K.170, N.171, H.173, Y.175, I.258 Chain C: R.158, K.170, N.171, H.173, Y.175 Ligands: FBP.5 14 PLIP interactions: 6 interactions with chain C, 8 interactions with chain B Hydrogen bonds: C:K.170, C:K.170, C:N.171, B:R.158, B:K.170, B:N.171, B:Y.175, B:Y.175 Salt bridges: C:R.158, C:H.173, C:H.173, B:R.158, B:H.173, B:H.173 FBP.5: 12 residues within 4Å: Chain B: R.158, K.170, N.171, H.173, Y.175 Chain C: R.158, K.170, N.171, H.173, Y.175, I.258 Ligands: FBP.3 17 PLIP interactions: 8 interactions with chain C, 9 interactions with chain B Hydrogen bonds: C:R.158, C:K.170, C:N.171, C:Y.175, C:Y.175, B:K.170, B:K.170, B:N.171, B:Y.175 Salt bridges: C:R.158, C:H.173, C:H.173, B:R.158, B:H.173, B:H.173 Water bridges: B:R.158, B:R.158 FBP.7: 12 residues within 4Å: Chain A: R.158, K.170, N.171, H.173, Y.175 Chain D: R.158, K.170, N.171, H.173, Y.175, I.258 Ligands: FBP.1 17 PLIP interactions: 8 interactions with chain D, 9 interactions with chain A Hydrogen bonds: D:R.158, D:K.170, D:N.171, D:Y.175, D:Y.175, A:K.170, A:K.170, A:N.171, A:Y.175 Salt bridges: D:R.158, D:H.173, D:H.173, A:R.158, A:H.173, A:H.173 Water bridges: A:R.158, A:R.158

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.2: 23 residues within 4Å: Chain A: G.14, G.16, A.17, V.18, E.38, D.39, I.40, R.44, T.82, A.83, G.84, P.85, R.86, I.103, I.107, I.123, T.124, N.125, S.148, H.180, I.230, N.237, I.240 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.230, A:I.240, A:I.240 Hydrogen bonds: A:A.17, A:V.18, A:I.40, A:R.44, A:G.84, A:I.123, A:N.125, A:S.148 Salt bridges: A:R.86 NAD.4: 23 residues within 4Å: Chain B: G.14, G.16, A.17, V.18, E.38, D.39, I.40, R.44, T.82, A.83, G.84, P.85, R.86, I.103, I.107, I.123, T.124, N.125, S.148, H.180, I.230, N.237, I.240 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.230, B:I.240, B:I.240 Hydrogen bonds: B:A.17, B:V.18, B:I.40, B:R.44, B:G.84, B:I.123, B:N.125, B:S.148 Salt bridges: B:R.86 NAD.6: 23 residues within 4Å: Chain C: G.14, G.16, A.17, V.18, E.38, D.39, I.40, R.44, T.82, A.83, G.84, P.85, R.86, I.103, I.107, I.123, T.124, N.125, S.148, H.180, I.230, N.237, I.240 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:I.230, C:I.240, C:I.240 Hydrogen bonds: C:A.17, C:V.18, C:I.40, C:R.44, C:G.84, C:I.123, C:N.125, C:S.148 Salt bridges: C:R.86 NAD.8: 23 residues within 4Å: Chain D: G.14, G.16, A.17, V.18, E.38, D.39, I.40, R.44, T.82, A.83, G.84, P.85, R.86, I.103, I.107, I.123, T.124, N.125, S.148, H.180, I.230, N.237, I.240 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:I.230, D:I.240, D:I.240 Hydrogen bonds: D:A.17, D:V.18, D:I.40, D:R.44, D:G.84, D:I.123, D:N.125, D:S.148 Salt bridges: D:R.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Iwata, S. et al., T and R states in the crystals of bacterial L-lactate dehydrogenase reveal the mechanism for allosteric control. Nat.Struct.Biol. (1994)

Release Date

1995-03-31

Peptides

L-LACTATE DEHYDROGENASE (T- AND R- STATE TETRAMER COMPLEX): ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
T

B
T

C
T

D
T

L-LACTATE DEHYDROGENASE (T- AND R- STATE TETRAMER COMPLEX)

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