SMTL ID : 7nut.1

Crystal structure of human AMDHD2 in complex with Zn and GlcN6P

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x GLP: 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose(Non-covalent)

GLP.1: 17 residues within 4Å: Chain A: G.153, A.154, H.155, H.211, H.232, N.235, A.236, I.267, H.272, D.294, T.327, L.328, S.329, G.330 Chain B: H.242, R.243 Ligands: ZN.2 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:A.154, A:N.235, A:A.236, A:D.294, A:S.329 Water bridges: A:K.151, A:M.237, B:R.243 Salt bridges: A:H.232, A:H.272, B:H.242, B:R.243 GLP.3: 17 residues within 4Å: Chain A: H.242, R.243 Chain B: G.153, A.154, H.155, H.211, H.232, N.235, A.236, I.267, H.272, D.294, T.327, L.328, S.329, G.330 Ligands: ZN.4 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:A.154, B:N.235, B:A.236, B:D.294, B:D.294, B:S.329 Water bridges: B:K.151, B:H.155 Salt bridges: B:H.232, B:H.272, A:H.242, A:R.243

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 7 residues within 4Å: Chain A: Q.71, E.143, H.155, H.211, T.231, H.232 Ligands: GLP.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.143, A:H.211, A:H.232, H2O.1, H2O.4 ZN.4: 7 residues within 4Å: Chain B: Q.71, E.143, H.155, H.211, T.231, H.232 Ligands: GLP.3 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.143, B:H.211, B:H.232, H2O.7, H2O.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kroef, V. et al., GFPT2/GFAT2 and AMDHD2 act in tandem to control the hexosamine pathway. Elife (2022)

Release Date

2021-04-28

Peptides

N-acetylglucosamine-6-phosphate deacetylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

N-acetylglucosamine-6-phosphate deacetylase

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