SMTL ID : 2g8y.1

The structure of a putative malate/lactate dehydrogenase from E. coli.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 9 residues within 4Å: Chain A: H.70, T.184, A.209, F.210, G.211 Ligands: SO4.3, NAD.4, EDO.8, EDO.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.184, A:F.210, A:G.211 Salt bridges: A:H.70 SO4.2: 4 residues within 4Å: Chain A: R.28, T.341, R.345, P.351 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.345 Salt bridges: A:R.28, A:R.345 SO4.3: 7 residues within 4Å: Chain A: H.67, D.68, S.69, H.70, A.209 Ligands: SO4.1, NAD.4 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.69, A:S.69, A:S.69, A:H.70 Water bridges: A:H.67, A:D.68, A:K.212, A:K.212 Salt bridges: A:H.67, A:H.70 SO4.11: 7 residues within 4Å: Chain B: H.67, D.68, S.69, H.70, A.209 Ligands: SO4.13, NAD.16 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:H.67, B:S.69, B:S.69 Water bridges: B:D.68, B:D.68, B:S.69 Salt bridges: B:H.67, B:H.70, B:K.212 SO4.12: 5 residues within 4Å: Chain B: P.76, S.77, R.80, R.214, A.359 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.77 Water bridges: B:R.214 Salt bridges: B:R.80, B:R.214 SO4.13: 8 residues within 4Å: Chain B: H.70, T.184, A.209, F.210, G.211 Ligands: SO4.11, NAD.16, EDO.18 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.184, B:F.210, B:G.211 Salt bridges: B:H.70 SO4.14: 2 residues within 4Å: Chain B: R.342, Q.346 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.346 Water bridges: B:R.342 Salt bridges: B:R.342 SO4.15: 2 residues within 4Å: Chain B: R.43, E.49 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.43, B:E.49, B:E.49, B:E.49 Salt bridges: B:R.43

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

NAD.4: 29 residues within 4Å: Chain A: H.67, H.70, H.142, G.144, R.145, I.146, V.166, T.184, P.186, L.200, L.201, D.202, Y.203, A.204, A.209, N.292, L.332, P.334, G.335, W.337, E.338 Chain B: F.175, H.176, H.256, K.257, Y.259 Ligands: SO4.1, SO4.3, EDO.9 31 PLIP interactions: 6 interactions with chain B, 25 interactions with chain A Water bridges: B:H.176, B:K.257, B:K.257, A:H.67, A:R.145, A:A.209, A:K.212, A:K.212, A:K.212, A:K.212, A:L.332, A:L.332, A:W.337 Salt bridges: B:H.256, B:K.257, A:H.67, A:K.212, A:K.212 pi-Cation interactions: B:H.256 Hydrophobic interactions: A:P.186, A:A.204 Hydrogen bonds: A:G.144, A:G.144, A:I.146, A:D.202, A:D.202, A:D.202, A:A.204, A:N.292, A:G.335, A:E.338 NAD.16: 28 residues within 4Å: Chain A: F.175, H.176, H.256, K.257, Y.259 Chain B: H.67, H.70, H.142, G.144, R.145, I.146, V.166, T.184, P.186, L.200, L.201, D.202, Y.203, A.204, A.209, N.292, L.332, P.334, G.335, E.338 Ligands: SO4.11, SO4.13, EDO.18 31 PLIP interactions: 23 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:P.186, B:A.204 Hydrogen bonds: B:G.144, B:I.146, B:D.202, B:D.202, B:D.202, B:A.204, B:N.292, B:N.292, B:G.335, B:E.338, A:H.176 Water bridges: B:H.67, B:A.209, B:K.212, B:K.212, B:K.212, B:L.332, B:L.332, B:W.337, B:E.338, A:K.257, A:K.257, A:K.257 Salt bridges: B:H.67, B:K.212, A:H.256, A:K.257, A:K.257 pi-Cation interactions: A:H.256

10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 4 residues within 4Å: Chain A: Q.243, E.244, S.245, L.247 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.243 EDO.6: 4 residues within 4Å: Chain A: A.31, Q.32, H.35, Q.346 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.346 EDO.7: 2 residues within 4Å: Chain A: H.176 Chain B: K.329 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.329 Water bridges: A:H.176 EDO.8: 5 residues within 4Å: Chain A: S.69, M.74, R.214 Ligands: SO4.1, EDO.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.214, A:R.214 EDO.9: 8 residues within 4Å: Chain A: H.70, H.142, M.171, T.184, I.290 Ligands: SO4.1, NAD.4, EDO.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.142, A:T.184 EDO.17: 6 residues within 4Å: Chain B: H.128, A.156, G.157, F.158, N.300, E.302 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.128, B:N.300, B:E.302 EDO.18: 7 residues within 4Å: Chain B: H.70, H.142, M.171, T.184, I.290 Ligands: SO4.13, NAD.16 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.142, B:T.184 Water bridges: B:T.184, B:T.184 EDO.19: 3 residues within 4Å: Chain B: R.28, E.344, R.345 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.28, B:R.28, B:R.345 EDO.20: 5 residues within 4Å: Chain A: Q.312 Chain B: K.276, H.279, E.281, T.282 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.276, B:E.281, A:Q.312 Water bridges: B:K.276 EDO.21: 3 residues within 4Å: Chain B: S.69, G.211, R.214 1 PLIP interactions: 1 interactions with chain B Water bridges: B:S.69

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.10: 2 residues within 4Å: Chain A: W.82, S.83 No protein-ligand interaction detected (PLIP)

Links

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Citation

Cuff, M.E. et al., The structure of a putative malate/lactate dehydrogenase from E. coli. To be Published

Release Date

2006-04-25

Peptides

Malate/L-lactate dehydrogenases: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Malate/L-lactate dehydrogenases