SMTL ID : 6jw7.1

The crystal structure of KanD2 in complex with NADH and 3"-deamino-3"-hydroxykanamycin A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

homo-tetramer

Ligands

4 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.1: 24 residues within 4Å: Chain A: G.11, A.12, G.13, F.14, M.15, D.36, L.37, T.73, T.74, P.75, N.76, L.78, H.79, Q.82, E.96, K.97, P.98, G.123, N.125, A.162, W.164, H.182, Y.310 Ligands: CJX.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:A.12, A:A.12, A:F.14, A:L.37, A:T.74, A:N.76, A:Q.82, A:N.125, A:Y.310 NAI.3: 22 residues within 4Å: Chain B: G.11, A.12, G.13, F.14, M.15, D.36, L.37, T.73, T.74, P.75, N.76, L.78, H.79, Q.82, E.96, K.97, P.98, N.125, A.162, W.164, H.182, Y.310 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:F.14, B:M.15, B:L.37, B:T.74, B:N.76, B:Q.82, B:E.96 NAI.4: 24 residues within 4Å: Chain C: G.11, A.12, G.13, F.14, M.15, D.36, L.37, T.73, T.74, P.75, N.76, L.78, H.79, Q.82, E.96, K.97, P.98, G.123, N.125, A.162, W.164, H.182, Y.310 Ligands: CJX.5 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:A.12, C:A.12, C:F.14, C:L.37, C:T.74, C:N.76, C:Q.82, C:E.96, C:N.125 NAI.6: 22 residues within 4Å: Chain D: G.11, A.12, G.13, F.14, M.15, D.36, L.37, T.73, T.74, P.75, N.76, L.78, H.79, Q.82, E.96, K.97, P.98, N.125, A.162, W.164, H.182, Y.310 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:F.14, D:M.15, D:L.37, D:T.74, D:N.76, D:Q.82, D:E.96, D:Y.310

2 x CJX: (2R,3S,4S,5R,6R)-2-(aminomethyl)-6-[(1R,2S,3S,4R,6S)-4,6-bis(azanyl)-3-[(2S,3R,4S,5S,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2-oxidanyl-cyclohexyl]oxy-oxane-3,4,5-triol(Non-covalent)

CJX.2: 15 residues within 4Å: Chain A: F.14, F.126, F.155, N.157, P.160, D.178, L.179, H.182, E.256, W.274, W.291, D.292, W.304, Y.310 Ligands: NAI.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.274, A:W.291, A:W.304 Hydrogen bonds: A:N.157, A:N.157, A:D.178, A:D.178, A:E.256, A:W.291, A:D.292 Water bridges: A:W.291 CJX.5: 15 residues within 4Å: Chain C: F.14, F.126, F.155, N.157, P.160, D.178, L.179, H.182, E.256, W.274, W.291, D.292, W.304, Y.310 Ligands: NAI.4 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:W.274, C:W.291, C:W.304 Hydrogen bonds: C:N.157, C:N.157, C:D.178, C:D.178, C:E.256, C:W.291, C:D.292, C:D.292, C:Y.310 Water bridges: C:W.291

Links

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Citation

Kudo, F. et al., Biochemical and structural analysis of a dehydrogenase, KanD2, and an aminotransferase, KanS2, that are responsible for the construction of the kanosamine moiety in kanamycin biosynthesis. Biochemistry (2020)

Release Date

2020-04-15

Peptides

Dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Dehydrogenase

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