SMTL ID : 5k4v.1

Three-dimensional structure of L-threonine 3-dehydrogenase from Trypanosoma brucei bound to NAD+ refined to 2.2 angstroms

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 27 residues within 4Å: Chain A: G.8, L.10, G.11, Q.12, I.13, D.34, V.35, L.53, D.54, C.55, L.76, P.77, A.78, M.80, I.94, P.116, S.117, T.118, Y.143, K.147, L.170, P.171, I.173, G.181, T.185 Ligands: ACT.7, NA.11 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:I.13, A:L.170 Hydrogen bonds: A:L.10, A:Q.12, A:Q.12, A:Q.12, A:I.13, A:V.35, A:D.54, A:D.54, A:C.55, A:L.76, A:Y.143, A:K.147, A:I.173, A:G.181, A:T.185 Water bridges: A:G.8, A:G.11, A:G.14, A:P.180 NAD.12: 27 residues within 4Å: Chain B: G.8, L.10, G.11, Q.12, I.13, D.34, V.35, L.53, D.54, C.55, L.76, P.77, A.78, M.80, I.94, P.116, S.117, T.118, Y.143, K.147, L.170, P.171, G.172, I.173, G.181 Ligands: ACT.13, NA.20 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:L.170 Hydrogen bonds: B:G.8, B:Q.12, B:Q.12, B:Q.12, B:I.13, B:G.14, B:V.35, B:D.54, B:C.55, B:L.56, B:L.76, B:Y.143, B:K.147, B:I.173 Water bridges: B:G.11, B:Q.12, B:G.181, B:T.185

8 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 4 residues within 4Å: Chain A: N.59, E.62, K.63, K.66 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.66 ACT.3: 4 residues within 4Å: Chain A: A.27, D.28, V.30, G.49 No protein-ligand interaction detected (PLIP) ACT.4: 3 residues within 4Å: Chain A: T.71, N.110, R.112 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.71 Hydrogen bonds: A:T.71, A:N.110, A:R.112 Water bridges: A:R.112 ACT.5: 2 residues within 4Å: Chain A: S.245, E.250 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.250 ACT.6: 7 residues within 4Å: Chain A: E.104, R.107, Y.157, Y.161 Chain B: P.88, D.89, M.92 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:P.88 Hydrogen bonds: B:D.89, A:E.104, A:Y.157 Salt bridges: A:R.107 ACT.7: 6 residues within 4Å: Chain A: M.80, S.81, T.118, Y.143, W.279 Ligands: NAD.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.279 Hydrogen bonds: A:S.81, A:T.118 ACT.13: 7 residues within 4Å: Chain B: M.80, S.81, T.118, I.119, Y.143, W.279 Ligands: NAD.12 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.119, B:W.279 Hydrogen bonds: B:T.118, B:T.118 ACT.14: 2 residues within 4Å: Chain A: T.237 Chain B: K.125 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Water bridges: A:Q.159, A:Q.159, A:T.237, A:T.237 Salt bridges: A:R.236, B:K.125

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 8 residues within 4Å: Chain A: D.16, S.175, A.176, A.177, Y.215, M.216, D.306, Q.310 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.16, A:A.176, A:A.177, A:Y.215, A:Y.215 Water bridges: A:D.16, A:T.178 GOL.9: 6 residues within 4Å: Chain A: R.158, L.231, L.234, T.235, R.236, T.237 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.158, A:L.234 GOL.10: 2 residues within 4Å: Chain A: Y.161, G.162 No protein-ligand interaction detected (PLIP) GOL.15: 7 residues within 4Å: Chain B: D.16, S.175, A.176, A.177, Y.215, M.216, P.217 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.176, B:A.177, B:Y.215 Water bridges: B:T.178 GOL.16: 4 residues within 4Å: Chain B: E.269, Q.273, K.274, N.277 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.269, B:K.274, B:N.277 GOL.17: 3 residues within 4Å: Chain B: D.57, N.59, G.60 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.57 GOL.18: 6 residues within 4Å: Chain B: R.158, L.231, L.234, T.235, R.236, T.237 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.158 Water bridges: B:R.158 GOL.19: 4 residues within 4Å: Chain B: K.132, D.133, D.134, N.287 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.133, B:D.134, B:D.134, B:N.287 Water bridges: B:D.133

2 x NA: SODIUM ION(Non-functional Binders)

NA.11: 6 residues within 4Å: Chain A: Q.12, M.80, P.180, T.185, D.186 Ligands: NAD.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.186 Water bridges: A:D.186 NA.20: 5 residues within 4Å: Chain B: Q.12, M.80, P.180, D.186 Ligands: NAD.12 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.12, B:T.185 Water bridges: B:G.181, B:T.185

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Adjogatse, E. et al., Structure and function of L-threonine-3-dehydrogenase from the parasitic protozoan Trypanosoma brucei revealed by X-ray crystallography and geometric simulations. Acta Crystallogr D Struct Biol (2018)

Release Date

2017-11-15

Peptides

L-threonine 3-dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

L-threonine 3-dehydrogenase

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