SMTL ID : 7jp2.1

Crystal structure of TP0037 from Treponema pallidum, a D-lactate dehydrogenase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.38 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 8 residues within 4Å: Chain A: M.57, F.59, T.82, Y.106, H.301, F.304, M.313 Chain B: W.140 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.106 Water bridges: A:A.83, A:A.83, A:H.301 EDO.2: 8 residues within 4Å: Chain A: W.140, Q.141, K.142, P.143 Chain B: R.14, E.15, E.16, Y.305 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.142 Water bridges: B:E.15 EDO.4: 7 residues within 4Å: Chain A: W.140 Chain B: M.57, T.82, Y.106, H.301, F.304, M.313 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.106 Water bridges: B:A.83, B:A.83 EDO.5: 10 residues within 4Å: Chain B: L.122, R.127, E.128, Y.234, A.259, G.260, A.261, E.294, R.295, I.297 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.259 Water bridges: B:R.127, B:E.128, B:Y.234, B:Y.234 EDO.6: 7 residues within 4Å: Chain A: R.136 Chain B: N.277, G.278, N.279, N.280, P.281, I.282 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.282 EDO.7: 8 residues within 4Å: Chain A: E.130, V.133, R.134 Chain B: R.127, V.291, I.296, I.297, Y.298 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:E.130, B:R.127, B:R.127, B:Y.298, B:Y.298

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 6 residues within 4Å: Chain A: T.306, E.307, T.308 Chain B: K.147, E.148, C.151 Ligand excluded by PLIP CL.8: 6 residues within 4Å: Chain A: K.147, E.148, C.151 Chain B: T.306, E.307, T.308 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deka, R.K. et al., Biophysical and Biochemical Characterization of TP0037, a d-Lactate Dehydrogenase, Supports an Acetogenic Energy Conservation Pathway in Treponema pallidum. Mbio (2020)

Release Date

2020-09-09

Peptides

D-lactate dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D-lactate dehydrogenase