SMTL ID : 1kny.1

KANAMYCIN NUCLEOTIDYLTRANSFERASE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: S.39, D.50, E.52 Ligands: APC.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.52, A:E.52 MG.4: 4 residues within 4Å: Chain B: S.39, D.50, E.52 Ligands: APC.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.52

2 x APC: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER(Non-covalent)

APC.2: 18 residues within 4Å: Chain A: Y.37, G.38, S.39, R.42, S.49, D.50, E.52, L.98, T.99, G.101, Q.102, T.186, T.187, S.188 Chain B: E.145, K.149 Ligands: MG.1, KAN.6 15 PLIP interactions: 3 interactions with chain B, 12 interactions with chain A Hydrogen bonds: B:K.149, B:K.149, B:N.152, A:S.39, A:S.39, A:S.39, A:R.42, A:S.49, A:S.49, A:D.50, A:T.187, A:S.188 Water bridges: A:Y.37, A:Q.102, A:Y.185 APC.5: 17 residues within 4Å: Chain A: E.145, K.149 Chain B: Y.37, G.38, S.39, R.42, S.49, D.50, E.52, L.98, T.99, Q.102, T.186, T.187, S.188 Ligands: KAN.3, MG.4 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.39, B:S.39, B:R.42, B:S.49, B:D.50, B:D.50, B:T.186, B:T.187, B:S.188, A:K.149, A:K.149 Water bridges: B:G.101

2 x KAN: KANAMYCIN A(Non-covalent)

KAN.3: 9 residues within 4Å: Chain A: S.94, D.95, E.141, E.142, E.145 Chain B: E.67, E.76 Ligands: APC.5, KAN.6 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.94, A:D.95, A:D.95, A:E.141, A:E.145, B:E.67 KAN.6: 10 residues within 4Å: Chain A: E.67, K.74, E.76 Chain B: S.94, D.95, E.141, E.142, E.145 Ligands: APC.2, KAN.3 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:E.67, A:K.74, B:S.94, B:D.95, B:E.141, B:E.142, B:E.145 Water bridges: A:E.76, A:E.76

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pedersen, L.C. et al., Structural investigation of the antibiotic and ATP-binding sites in kanamycin nucleotidyltransferase. Biochemistry (1995)

Release Date

1996-08-17

Peptides

KANAMYCIN NUCLEOTIDYLTRANSFERASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

KANAMYCIN NUCLEOTIDYLTRANSFERASE