SMTL ID : 2a2c.1

x-ray structure of human N-acetyl galactosamine kinase complexed with Mg-ADP and N-acetyl galactosamine 1-phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

1 x NG1: 2-acetamido-2-deoxy-1-O-phosphono-alpha-D-galactopyranose(Non-covalent)

NG1.1: 20 residues within 4Å: Chain A: R.63, E.69, H.70, D.72, Y.73, G.163, S.165, S.168, E.199, G.206, G.207, M.209, D.210, Q.211, K.254, F.260, G.421, A.422 Ligands: MG.2, ADP.5 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:E.69, A:H.70, A:D.72, A:G.163, A:S.165, A:G.206, A:G.207, A:G.207, A:D.210, A:A.422 Water bridges: A:I.71, A:S.167, A:D.210, A:D.210, A:D.210, A:Q.211 Salt bridges: A:R.63, A:R.63, A:K.254

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: S.167 Ligands: NG1.1, ADP.5 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.167, H2O.1, H2O.1

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

CL.3: 2 residues within 4Å: Chain A: L.126, W.127 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 3 residues within 4Å: Chain A: F.227, S.228, R.231 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.227, A:R.231 Water bridges: A:E.226

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.5: 19 residues within 4Å: Chain A: N.103, Y.108, W.127, Y.130, G.156, P.160, S.161, S.162, G.163, L.164, S.165, S.166, S.167, L.170, M.252, N.253, K.254 Ligands: NG1.1, MG.2 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:N.103, A:G.156, A:G.156, A:S.161, A:S.161, A:S.162, A:G.163, A:L.164, A:S.165, A:S.166, A:S.167, A:S.167, A:N.253, A:K.254 Water bridges: A:P.125, A:P.125, A:W.127, A:Y.130, A:Y.130, A:S.161, A:S.168, A:A.255 Salt bridges: A:K.254, A:K.254 pi-Stacking: A:Y.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thoden, J.B. et al., The molecular architecture of human N-acetylgalactosamine kinase. J.Biol.Chem. (2005)

Release Date

2005-07-26

Peptides

N-acetylgalactosamine kinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

N-acetylgalactosamine kinase

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