SMTL ID : 6jw6.1

The crystal structure of KanD2 in complex with NAD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 23 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 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:A.12, A:A.12, A:G.13, A:F.14, A:M.15, A:L.37, A:T.74, A:N.76, A:Q.82, A:N.125, A:N.125, A:Y.310 NAD.2: 21 residues within 4Å: Chain B: G.11, G.13, F.14, M.15, D.36, L.37, T.73, T.74, P.75, N.76, H.79, Q.82, E.96, K.97, P.98, N.125, F.126, A.162, W.164, H.182, Y.310 8 PLIP interactions: 8 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, B:E.96 NAD.3: 23 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 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:A.12, C:A.12, C:G.13, C:F.14, C:M.15, C:L.37, C:T.74, C:N.76, C:Q.82, C:E.96, C:N.125, C:N.125 NAD.4: 21 residues within 4Å: Chain D: G.11, G.13, F.14, M.15, D.36, L.37, T.73, T.74, P.75, N.76, H.79, Q.82, E.96, K.97, P.98, N.125, F.126, 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

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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