SMTL ID : 3ec7.4 (5 other biounits)

Crystal Structure of Putative Dehydrogenase from Salmonella typhimurium LT2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 24 residues within 4Å: Chain A: 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, 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:I.34, A:W.292 Hydrogen bonds: A:I.31, A:I.34, A:I.57, A:R.61, A:A.95, A:S.96, A:N.97 Water bridges: A:G.32, A:G.35, A:N.97, A:H.197 NAD.5: 24 residues within 4Å: Chain B: 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, W.292, Y.300 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.34, B:W.292 Hydrogen bonds: B:I.34, B:I.57, B:R.61, B:A.95, B:S.96, B:N.97, B:Y.300 Water bridges: B:G.32, B:G.35, B:H.197 NAD.7: 26 residues within 4Å: Chain C: V.29, G.30, I.31, 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 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:I.34, C:W.292 Hydrogen bonds: C:I.34, C:G.35, C:I.57, C:V.58, C:R.61, C:A.95, C:S.96, C:N.97, C:Y.300 Water bridges: C:G.32 NAD.10: 23 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, H.100, E.117, K.118, P.119, G.145, M.147, W.292, Y.300 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:W.292 Hydrogen bonds: D:I.31, D:I.34, D:I.57, D:A.95, D:S.96, D:N.97 Water bridges: D:G.32, D:G.35, D:N.97 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 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:V.182, A:H.197, A:Y.255 Water bridges: A:K.118, A:N.178, A:W.292 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 Water bridges: B:K.118, B:R.148 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 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:V.182, C:H.197 Salt bridges: C:E.193, C:E.193 EPE.11: 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

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

EDO.3: 8 residues within 4Å: Chain A: S.275, A.276, A.277, V.278, S.285, T.286, D.287 Chain C: K.283 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:S.275, A:S.275, A:S.285, D:Q.156 EDO.4: 5 residues within 4Å: Chain A: Y.192, D.333, V.336, K.337, E.340 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.192 Water bridges: A:Y.192, A:D.333 EDO.9: 8 residues within 4Å: Chain B: A.274 Chain C: D.151, G.153, L.270, P.271, T.272, V.273, R.295 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:D.151, C:G.153, C:R.295, C:R.295 Water bridges: C:K.152, C:A.274, B:A.274 EDO.12: 9 residues within 4Å: Chain A: Q.156, I.160 Chain B: K.283 Chain D: S.275, A.276, V.278, S.285, T.286, D.287 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:S.285, D:D.287, A:Q.156

1 x K: POTASSIUM ION(Non-covalent)

K.13: 1 residues within 4Å: Chain D: D.333 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
E

B
F

C
G

D
H

Putative Dehydrogenase

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