SMTL ID : 8du1.1 (1 other biounit)

Crystal Structure of NAD bound dTDP-glucose 4,6-dehydratase from Elizabethkingia anophelis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: Y.46, A.47, F.211, K.214 Ligands: NAD.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.214 Water bridges: A:F.20, A:Y.46, A:S.94, A:S.94, A:K.214 EDO.3: 6 residues within 4Å: Chain A: I.12, N.33, I.36, H.252, F.255, N.256 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.33, A:H.252, A:N.256 EDO.4: 8 residues within 4Å: Chain A: G.207, N.209, H.210, P.217, T.339, W.342, Y.343, W.349 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.209, A:H.210, A:H.210 Water bridges: A:G.207, A:H.210 EDO.7: 5 residues within 4Å: Chain B: Y.46, A.47, F.211, K.214 Ligands: NAD.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.214 Water bridges: B:F.20 EDO.9: 7 residues within 4Å: Chain B: I.12, F.29, N.33, I.36, H.252, F.255, N.256 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.33, B:H.252, B:N.256 Water bridges: B:N.256 EDO.10: 8 residues within 4Å: Chain B: G.207, N.209, H.210, P.217, T.339, W.342, Y.343, W.349 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.209, B:H.210, B:H.210 Water bridges: B:G.207, B:G.207

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

NAD.2: 30 residues within 4Å: Chain A: G.16, A.18, G.19, F.20, I.21, G.22, D.42, A.43, L.44, T.45, A.47, G.48, A.67, D.68, I.69, T.70, L.90, A.91, A.92, T.109, V.148, S.149, T.150, Y.175, K.179, C.202, S.203, N.204, N.205 Ligands: EDO.1 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:I.21 Hydrogen bonds: A:A.18, A:A.18, A:F.20, A:I.21, A:G.22, A:A.43, A:L.44, A:T.45, A:T.45, A:A.47, A:I.69, A:L.90, A:A.92, A:T.109, A:Y.175, A:K.179, A:N.205, A:N.205 Water bridges: A:G.19, A:T.45, A:T.70, A:S.94 NAD.8: 30 residues within 4Å: Chain B: G.16, A.18, G.19, F.20, I.21, G.22, D.42, A.43, L.44, T.45, A.47, G.48, A.67, D.68, I.69, L.90, A.91, A.92, E.93, T.109, V.148, S.149, T.150, Y.175, K.179, C.202, S.203, N.204, N.205 Ligands: EDO.7 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:I.21 Hydrogen bonds: B:A.18, B:A.18, B:F.20, B:I.21, B:G.22, B:A.43, B:L.44, B:T.45, B:T.45, B:A.47, B:G.48, B:D.68, B:I.69, B:L.90, B:A.92, B:Y.175, B:K.179, B:N.205, B:N.205 Water bridges: B:G.19, B:S.94

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

CL.5: 3 residues within 4Å: Chain A: Y.232, G.235, N.274 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain B: Y.232, G.235, N.274, H.309 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 2 residues within 4Å: Chain B: D.316, T.318 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.318, H2O.19, H2O.22, H2O.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

DeBouver, N.D. et al., Crystal Structure of DNA Polymerase III beta subunit from Elizabethkingia anophelis. to be published

Release Date

2022-08-10

Peptides

dTDP-glucose 4,6-dehydratase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

dTDP-glucose 4,6-dehydratase

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