SMTL ID : 3ec7.1 (5 other biounits)

Crystal Structure of Putative Dehydrogenase from Salmonella typhimurium LT2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 25 residues within 4Å: Chain A: V.29, G.30, G.32, M.33, I.34, C.55, D.56, I.57, V.58, R.61, Y.79, T.94, A.95, S.96, N.97, A.99, H.100, E.117, K.118, P.119, G.145, M.147, H.197, W.292, Y.300 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.292 Hydrogen bonds: A:I.34, A:I.57, A:R.61, A:A.95, A:S.96, A:N.97, A:Y.300 Water bridges: A:G.32, A:G.35, A:D.56, A:D.56, A:H.197 NAD.5: 27 residues within 4Å: Chain B: V.29, G.30, I.31, G.32, M.33, I.34, G.35, C.55, D.56, I.57, V.58, R.61, Y.79, T.94, A.95, S.96, N.97, A.99, H.100, E.117, K.118, P.119, G.145, M.147, H.197, W.292, Y.300 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:I.34, B:K.118, B:W.292 Hydrogen bonds: B:I.31, B:I.34, B:G.35, B:I.57, B:R.61, B:A.95, B:S.96, B:N.97 Water bridges: B:G.32, B:N.97 NAD.7: 23 residues within 4Å: Chain C: V.29, G.30, G.32, M.33, I.34, C.55, D.56, I.57, V.58, R.61, Y.79, T.94, A.95, S.96, N.97, A.99, H.100, E.117, K.118, P.119, G.145, M.147, Y.300 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:I.34 Hydrogen bonds: C:I.34, C:G.35, C:I.57, C:R.61, C:A.95, C:S.96, C:N.97 Water bridges: C:G.32 NAD.9: 24 residues within 4Å: Chain D: V.29, G.30, I.31, G.32, M.33, I.34, C.55, D.56, I.57, V.58, R.61, T.94, A.95, S.96, N.97, A.99, H.100, E.117, K.118, P.119, G.145, M.147, W.292, Y.300 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:W.292 Hydrogen bonds: D:I.31, D:I.34, D:I.57, D:R.61, D:A.95, D:S.96, D:N.97, D:Y.300 Water bridges: D:G.32, D:G.35, D:N.97, D:K.118 pi-Cation interactions: D:K.118

4 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.2: 10 residues within 4Å: Chain A: H.176, N.178, T.181, V.182, Y.185, E.193, T.194, H.197, Y.255, W.292 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.182, A:H.197 Water bridges: A:K.118, A:N.178 Salt bridges: A:E.193, A:E.193 EPE.6: 10 residues within 4Å: Chain B: H.176, N.178, T.181, V.182, Y.185, E.193, T.194, H.197, Y.255, W.292 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:V.182, B:H.197, B:Y.255 Water bridges: B:N.178 Salt bridges: B:E.193, B:E.193 EPE.8: 10 residues within 4Å: Chain C: H.176, N.178, T.181, V.182, Y.185, E.193, T.194, H.197, Y.255, W.292 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:V.182, C:H.197, C:Y.255 Water bridges: C:N.178 Salt bridges: C:E.193, C:E.193 EPE.10: 10 residues within 4Å: Chain D: H.176, N.178, T.181, V.182, Y.185, E.193, T.194, H.197, Y.255, W.292 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:V.182, D:H.197 Water bridges: D:N.178 Salt bridges: D:E.193, D:E.193

2 x ACY: ACETIC ACID(Non-functional Binders)

ACY.3: 4 residues within 4Å: Chain A: D.333, V.336, K.337, E.340 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.337 ACY.4: 5 residues within 4Å: Chain A: Q.252, Y.253, V.290 Chain C: A.281, A.282 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:A.282 Water bridges: C:A.281

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

EDO.11: 9 residues within 4Å: Chain A: Q.156 Chain B: K.283 Chain D: S.275, A.276, A.277, V.278, S.285, T.286, D.287 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D, 1 interactions with chain B Hydrogen bonds: A:Q.156, D:S.275, D:D.287, B:K.283 Water bridges: A:E.165

1 x K: POTASSIUM ION(Non-covalent)

K.12: 1 residues within 4Å: Chain D: E.340 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Crystal Structure of Putative Dehydrogenase from Salmonella typhimurium LT2. To be Published

Release Date

2008-09-23

Peptides

Putative Dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Putative Dehydrogenase

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