SMTL ID : 6fwz.1

Crystal structure of human UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase (DPAGT1) (V264G mutant) in complex with UDP-GlcNAc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: N.186, D.253 Ligands: UD1.2 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.253, H2O.1, H2O.1 MG.5: 3 residues within 4Å: Chain B: N.186, D.253 Ligands: UD1.6 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.253, H2O.2, H2O.2

2 x UD1: URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE(Non-covalent)

UD1.2: 20 residues within 4Å: Chain A: G.44, Q.45, D.46, L.47, E.57, N.186, I.187, A.189, G.190, I.191, N.192, E.195, F.250, D.253, L.294, R.302, H.303, R.304, I.305 Ligands: MG.1 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:I.187, A:F.250, A:L.294 Hydrogen bonds: A:Q.45, A:D.46, A:D.46, A:L.47, A:N.48, A:N.186, A:N.192, A:R.304, A:R.304, A:R.304, A:I.305 Water bridges: A:N.48, A:N.48, A:G.193, A:E.195, A:E.195, A:D.253, A:D.253 Salt bridges: A:K.126, A:R.302, A:R.302, A:R.302, A:H.303, A:H.303 UD1.6: 20 residues within 4Å: Chain B: G.44, Q.45, D.46, L.47, E.57, N.186, I.187, A.189, G.190, I.191, N.192, E.195, F.250, D.253, L.294, R.302, H.303, R.304, I.305 Ligands: MG.5 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:I.187, B:F.250, B:L.294 Hydrogen bonds: B:Q.45, B:D.46, B:L.47, B:N.48, B:N.186, B:N.192, B:H.303, B:R.304, B:R.304, B:R.304, B:I.305 Water bridges: B:N.48, B:N.48, B:G.193, B:E.195, B:D.253, B:D.253, B:D.253, B:D.253 Salt bridges: B:K.126, B:R.302, B:R.302, B:R.302, B:H.303, B:H.303

2 x UNL: UNKNOWN LIGAND

UNL.3: 5 residues within 4Å: Chain A: L.176, H.271, S.273, K.274, L.288 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.176, A:K.274, A:L.288 UNL.7: 5 residues within 4Å: Chain B: L.176, H.271, S.273, K.274, L.288 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.176, B:K.274, B:L.288

2 x P6L: (2S)-3-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-[(6E)-HEXADEC-6-ENOYLOXY]PROPYL (8E)-OCTADEC-8-ENOATE(Non-covalent)

P6L.4: 6 residues within 4Å: Chain A: A.204, L.240, W.244, Y.245, R.378, L.382 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.204, A:L.240 Hydrogen bonds: A:W.244 Salt bridges: A:R.378 P6L.8: 6 residues within 4Å: Chain B: A.204, L.240, W.244, Y.245, R.378, L.382 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.204, B:L.240 Hydrogen bonds: B:W.244 Salt bridges: B:R.378

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dong, Y.Y. et al., Structures of DPAGT1 Explain Glycosylation Disease Mechanisms and Advance TB Antibiotic Design. Cell (2018)

Release Date

2018-07-25

Peptides

UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Membrane

We predict this structure to be a membrane protein.
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UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase

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