SMTL ID : 2ejv.1

Crystal structure of threonine 3-dehydrogenase complexed with NAD+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.38, H.63, E.64, E.148 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.38, A:H.63, A:E.64 ZN.2: 5 residues within 4Å: Chain A: C.93, H.94, C.96, C.99, C.107 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.93, A:C.96, A:C.99, A:C.107 ZN.4: 4 residues within 4Å: Chain B: C.38, H.63, E.64, E.148 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.38, B:H.63, B:E.64 ZN.5: 5 residues within 4Å: Chain B: C.93, H.94, C.96, C.99, C.107 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.93, B:C.96, B:C.99, B:C.107 ZN.7: 4 residues within 4Å: Chain C: C.38, H.63, E.64, E.148 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.38, C:H.63, C:E.64 ZN.8: 5 residues within 4Å: Chain C: C.93, H.94, C.96, C.99, C.107 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.93, C:C.96, C:C.99, C:C.107 ZN.10: 4 residues within 4Å: Chain D: C.38, H.63, E.64, E.148 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.38, D:H.63, D:E.64 ZN.11: 5 residues within 4Å: Chain D: C.93, H.94, C.96, C.99, C.107 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.93, D:C.96, D:C.99, D:C.107

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

NAD.3: 22 residues within 4Å: Chain A: N.152, G.172, G.174, P.175, I.176, S.195, D.196, P.197, N.198, R.201, P.215, F.238, S.239, N.241, A.244, L.261, G.262, I.263, I.286, A.287, G.288 Chain B: V.277 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.176, A:L.261 Hydrogen bonds: A:G.174, A:I.176, A:G.177, A:R.201, A:R.201, A:N.241, A:L.261, A:I.263, A:G.288 NAD.6: 23 residues within 4Å: Chain A: V.277 Chain B: N.152, G.172, G.174, P.175, I.176, G.177, S.195, D.196, P.197, N.198, R.201, P.215, F.238, S.239, N.241, A.244, L.261, G.262, I.263, I.286, A.287, G.288 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:I.176, B:L.261 Hydrogen bonds: B:G.174, B:I.176, B:G.177, B:R.201, B:S.239, B:N.241, B:L.261, B:I.263, B:G.288 Water bridges: B:Q.247 Salt bridges: B:R.201 NAD.9: 22 residues within 4Å: Chain C: N.152, G.172, G.174, P.175, I.176, S.195, D.196, P.197, N.198, R.201, P.215, F.238, S.239, N.241, A.244, L.261, G.262, I.263, I.286, A.287, G.288 Chain D: V.277 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:I.176, C:L.261 Hydrogen bonds: C:G.174, C:I.176, C:G.177, C:R.201, C:R.201, C:N.241, C:L.261, C:I.263, C:G.288 NAD.12: 23 residues within 4Å: Chain C: V.277 Chain D: N.152, G.172, G.174, P.175, I.176, G.177, S.195, D.196, P.197, N.198, R.201, P.215, F.238, S.239, N.241, A.244, L.261, G.262, I.263, I.286, A.287, G.288 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:I.176, D:L.261 Hydrogen bonds: D:G.174, D:I.176, D:G.177, D:R.201, D:S.239, D:N.241, D:L.261, D:I.263, D:G.288 Water bridges: D:Q.247 Salt bridges: D:R.201

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Omi, R. et al., Crystal structure of threonine 3-dehydrogenase. To be Published

Release Date

2008-03-25

Peptides

L-threonine 3-dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

L-threonine 3-dehydrogenase

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