SMTL ID : 5o5e.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.40 Å

Oligo State

homo-dimer

Ligands

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.1: 6 residues within 4Å: Chain A: V.201, A.204, V.208, W.244, R.378, S.392 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.201, A:V.208, A:W.244 Salt bridges: A:R.378 P6L.4: 6 residues within 4Å: Chain B: V.201, A.204, V.208, W.244, R.378, S.392 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.201, B:V.208, B:W.244 Salt bridges: B:R.378

2 x 9LH: Tunicamycin(Non-covalent)

9LH.2: 26 residues within 4Å: Chain A: Q.45, D.46, L.47, E.57, W.123, K.126, L.127, L.176, F.180, N.183, N.186, I.187, A.189, G.190, I.191, N.192, E.195, F.250, D.253, F.287, L.294, R.302, H.303, R.304, I.305 Ligands: UNL.3 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:W.123, A:L.127, A:L.176, A:F.180, A:N.183, A:I.187, A:F.287, A:L.294 Hydrogen bonds: A:Q.45, A:L.47, A:E.57, A:K.126, A:N.186, A:N.186, A:N.192, A:D.253, A:R.302, A:R.304, A:R.304, A:R.304, A:I.305 Water bridges: A:N.48, A:N.48, A:G.193, A:D.253 Salt bridges: A:R.302, A:R.302, A:H.303 pi-Stacking: A:F.250 9LH.5: 26 residues within 4Å: Chain B: Q.45, D.46, L.47, E.57, W.123, K.126, L.127, L.176, F.180, N.183, N.186, I.187, A.189, G.190, I.191, N.192, E.195, F.250, D.253, F.287, L.294, R.302, H.303, R.304, I.305 Ligands: UNL.6 31 PLIP interactions: 31 interactions with chain B Hydrophobic interactions: B:W.123, B:L.127, B:L.176, B:F.180, B:N.183, B:I.187, B:F.287, B:L.294 Hydrogen bonds: B:Q.45, B:L.47, B:E.57, B:K.126, B:N.186, B:N.186, B:N.192, B:D.253, B:R.302, 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:D.253, B:D.253 Salt bridges: B:R.302, B:R.302, B:H.303 pi-Stacking: B:F.250

2 x UNL: UNKNOWN LIGAND

UNL.3: 6 residues within 4Å: Chain A: Y.170, L.176, L.177, F.287, L.288 Ligands: 9LH.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.176, A:L.177, A:F.287, A:L.288 UNL.6: 6 residues within 4Å: Chain B: Y.170, L.176, L.177, F.287, L.288 Ligands: 9LH.5 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.176, B:L.177, B:F.287, B:L.288

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

2018-02-28

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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