SMTL ID : 1zem.3 (2 other biounits)

Crystal Structure of NAD+-Bound Xylitol Dehydrogenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-octamer

Ligands

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

NAD.1: 22 residues within 4Å: Chain A: G.14, G.16, G.17, N.18, I.19, D.38, M.39, C.63, D.64, V.65, N.91, A.92, G.93, I.115, T.142, A.143, S.144, Y.157, K.161, P.187, G.188, M.190 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:P.187 Hydrogen bonds: A:G.14, A:G.16, A:N.18, A:I.19, A:M.39, A:D.64, A:V.65, A:N.91, A:N.91, A:G.93, A:K.161, A:M.190 Water bridges: A:G.17, A:N.18, A:N.18, A:G.20, A:M.190 NAD.2: 24 residues within 4Å: Chain B: G.14, G.16, G.17, N.18, I.19, D.38, M.39, N.40, C.63, D.64, V.65, T.66, N.91, A.92, G.93, I.115, T.142, A.143, S.144, Y.157, K.161, P.187, G.188, M.190 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:P.187 Hydrogen bonds: B:G.14, B:N.18, B:I.19, B:M.39, B:D.64, B:D.64, B:V.65, B:N.91, B:N.91, B:G.93, B:Y.157, B:K.161, B:M.190 Water bridges: B:N.18, B:G.20, B:N.40, B:M.190 NAD.5: 24 residues within 4Å: Chain C: G.14, G.16, G.17, N.18, I.19, D.38, M.39, N.40, C.63, D.64, V.65, N.91, A.92, G.93, I.115, T.142, A.143, S.144, Y.157, K.161, P.187, G.188, M.190, M.195 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:P.187 Hydrogen bonds: C:G.14, C:N.18, C:N.18, C:I.19, C:M.39, C:D.64, C:V.65, C:N.91, C:N.91, C:G.93, C:K.161, C:M.190 Water bridges: C:G.20, C:G.93, C:Y.94, C:M.190, C:M.190 NAD.7: 25 residues within 4Å: Chain D: G.14, G.16, G.17, N.18, I.19, D.38, M.39, N.40, C.63, D.64, V.65, T.66, N.91, A.92, G.93, I.115, T.142, A.143, S.144, Y.157, K.161, P.187, G.188, M.190, M.195 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:P.187 Hydrogen bonds: D:G.14, D:N.18, D:I.19, D:M.39, D:D.64, D:D.64, D:V.65, D:N.91, D:N.91, D:G.93, D:Y.157, D:K.161, D:M.190 Water bridges: D:G.17, D:N.18, D:G.20, D:N.40, D:G.93, D:M.190, D:F.194 NAD.9: 23 residues within 4Å: Chain E: G.14, G.16, G.17, N.18, I.19, D.38, M.39, C.63, D.64, V.65, N.91, A.92, G.93, I.115, T.142, A.143, S.144, Y.157, K.161, P.187, G.188, M.190, M.195 16 PLIP interactions: 16 interactions with chain E Hydrophobic interactions: E:P.187 Hydrogen bonds: E:G.14, E:N.18, E:I.19, E:M.39, E:D.64, E:V.65, E:N.91, E:N.91, E:G.93, E:K.161, E:M.190 Water bridges: E:G.17, E:N.18, E:G.20, E:F.194 NAD.11: 23 residues within 4Å: Chain F: G.14, G.16, G.17, N.18, I.19, D.38, M.39, C.63, D.64, V.65, T.66, N.91, A.92, G.93, I.115, T.142, A.143, S.144, Y.157, K.161, P.187, G.188, M.190 18 PLIP interactions: 18 interactions with chain F Hydrophobic interactions: F:P.187 Hydrogen bonds: F:G.14, F:N.18, F:I.19, F:M.39, F:D.64, F:D.64, F:V.65, F:N.91, F:N.91, F:G.93, F:Y.157, F:K.161, F:M.190 Water bridges: F:G.17, F:G.20, F:G.93, F:Y.94 NAD.12: 23 residues within 4Å: Chain G: G.14, G.16, G.17, N.18, I.19, D.38, M.39, C.63, D.64, V.65, N.91, A.92, G.93, I.115, T.142, A.143, S.144, Y.157, K.161, P.187, G.188, M.190, M.195 15 PLIP interactions: 15 interactions with chain G Hydrophobic interactions: G:P.187 Hydrogen bonds: G:G.14, G:N.18, G:I.19, G:M.39, G:D.64, G:V.65, G:N.91, G:N.91, G:G.93, G:K.161, G:M.190 Water bridges: G:G.17, G:G.20, G:M.190 NAD.13: 23 residues within 4Å: Chain H: G.14, G.16, G.17, N.18, I.19, D.38, M.39, C.63, D.64, V.65, N.91, A.92, G.93, I.115, T.142, A.143, S.144, Y.157, K.161, P.187, G.188, M.190, M.195 17 PLIP interactions: 17 interactions with chain H Hydrophobic interactions: H:P.187 Hydrogen bonds: H:G.14, H:N.18, H:N.18, H:I.19, H:M.39, H:D.64, H:D.64, H:V.65, H:N.91, H:N.91, H:G.93, H:Y.157, H:K.161, H:M.190 Water bridges: H:G.17, H:G.20

5 x MG: MAGNESIUM ION(Non-functional Binders)

MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ehrensberger, A.H. et al., Structure-guided engineering of xylitol dehydrogenase cosubstrate specificity. Structure (2006)

Release Date

2006-03-28

Peptides

xylitol dehydrogenase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

xylitol dehydrogenase

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