SMTL ID : 6svm.1

Crystal structure of human GFAT-1 in complex with Glucose-6-Phosphate, L-Glu, and UDP-GalNAc

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.48 Å

Oligo State

homo-dimer

Ligands

2 x G6Q: GLUCOSE-6-PHOSPHATE(Non-covalent)

G6Q.1: 20 residues within 4Å: Chain A: C.380, G.381, T.382, S.383, L.426, S.427, Q.428, S.429, G.430, T.432, T.435, V.478, A.479, S.480, Q.487, L.563, K.564, E.567 Chain B: H.583, G.584 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.382, A:S.383, A:S.383, A:S.427, A:Q.428, A:S.429, A:S.429, A:T.432, A:S.480, A:K.564, B:H.583, B:H.583 Water bridges: A:S.383, A:L.426, A:T.435, A:V.478, A:S.480 G6Q.5: 21 residues within 4Å: Chain A: H.583, G.584 Chain B: C.380, G.381, T.382, S.383, S.427, Q.428, S.429, G.430, E.431, T.432, V.478, A.479, S.480, Q.487, L.563, K.564, E.567, S.683, V.684 16 PLIP interactions: 2 interactions with chain A, 14 interactions with chain B Hydrogen bonds: A:H.583, A:H.583, B:T.382, B:T.382, B:S.383, B:S.383, B:S.427, B:Q.428, B:Q.428, B:S.429, B:S.429, B:S.429, B:T.432, B:S.480, B:S.480, B:K.564

1 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.2: 15 residues within 4Å: Chain A: C.2, H.93, R.95, W.96, A.97, T.98, H.99, H.108, H.122, N.123, G.124, I.125, T.147, D.148, T.149 13 PLIP interactions: 1 Ligand-Ligand interactions, 12 interactions with chain A Hydrogen bonds: E.2, A:C.2, A:W.96, A:T.98, A:T.98, A:T.98, A:H.99, A:G.124, A:G.124, A:D.148 Salt bridges: A:H.93, A:R.95, A:H.108

2 x UD2: URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE(Non-covalent)

UD2.3: 15 residues within 4Å: Chain A: Q.316, R.349, G.360, G.361, G.451, T.453, V.456, I.460, S.461, T.464, C.466, G.467, V.468, H.469 Ligands: MG.4 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.456 Hydrogen bonds: A:Q.316, A:G.361, A:T.464, A:G.467, A:H.469, A:H.469 Water bridges: A:R.349, A:G.360 Salt bridges: A:R.349, A:R.349, A:H.469 UD2.6: 15 residues within 4Å: Chain B: R.349, G.360, G.361, L.362, G.451, T.453, V.456, I.460, S.461, T.464, C.466, G.467, V.468, H.469 Ligands: MG.7 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.360, B:G.361, B:G.361, B:T.453, B:T.464, B:G.467, B:H.469 Salt bridges: B:R.349, B:R.349, B:H.469

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: S.461, R.462, T.464 Ligands: UD2.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:S.461, A:R.462, A:T.464 MG.7: 4 residues within 4Å: Chain B: S.461, R.462, T.464 Ligands: UD2.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:S.461, B:R.462, B:T.464

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ruegenberg, S. et al., Loss of GFAT-1 feedback regulation activates the hexosamine pathway that modulates protein homeostasis. Nat Commun (2020)

Release Date

2020-01-15

Peptides

Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1

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