SMTL ID : 4wh3.1

N-acetylhexosamine 1-kinase in complex with ATP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 21 residues within 4Å: Chain A: G.28, D.29, G.30, H.31, I.32, N.33, T.35, I.46, Q.48, L.80, Y.102, K.103, F.104, I.105, N.213, I.227, D.228, D.230 Ligands: MG.2, MG.3, GOL.4 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:D.29, A:D.29, A:H.31, A:I.32, A:N.33, A:N.33, A:Q.48, A:K.103, A:I.105, A:D.230 Water bridges: A:T.35, A:S.110, A:D.208, A:N.212, A:N.213

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: N.213, D.228 Ligands: ATP.1, MG.3 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.228, H2O.3, H2O.3 MG.3: 4 residues within 4Å: Chain A: D.228 Ligands: ATP.1, MG.2, ACY.9 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.228, A:D.228, H2O.3, H2O.3

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: Y.27, F.104, T.108, V.109, S.110, L.215 Ligands: ATP.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.27, A:Y.27, A:V.109 Water bridges: A:S.110, A:S.110 GOL.5: 10 residues within 4Å: Chain A: E.144, H.148, F.149, H.150, D.151, M.192, P.234, G.235, F.239 Ligands: GOL.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.148, A:H.150 Water bridges: A:H.148, A:D.151 GOL.6: 7 residues within 4Å: Chain A: N.207, D.208, K.210, D.243, R.246, F.247 Ligands: ACY.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.208, A:K.210, A:D.243, A:R.246 GOL.7: 6 residues within 4Å: Chain A: A.126, D.129, F.130, A.223, R.224, I.226 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.130 Water bridges: A:R.224 GOL.8: 6 residues within 4Å: Chain A: E.144, L.195, L.202, P.234, G.235 Ligands: GOL.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.144 Water bridges: A:L.142

2 x ACY: ACETIC ACID(Non-functional Binders)

ACY.9: 4 residues within 4Å: Chain A: F.55, T.231 Ligands: MG.3, GOL.6 No protein-ligand interaction detected (PLIP) ACY.10: 4 residues within 4Å: Chain A: S.140, Q.141, L.142, T.143 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.142 Salt bridges: A:R.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sato, M. et al., Open-close structural change upon ligand binding and two magnesium ions required for the catalysis of N-acetylhexosamine 1-kinase. Biochim.Biophys.Acta (2015)

Release Date

2015-02-18

Peptides

N-acetylhexosamine 1-kinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

N-acetylhexosamine 1-kinase

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