SMTL ID : 6bw5.1 (1 other biounit)

Human GPT (DPAGT1) in complex with tunicamycin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-dimer

Ligands

2 x TUM: Tunicamycin(Non-covalent)

TUM.1: 31 residues within 4Å: Chain A: G.43, Q.44, D.45, L.46, N.47, E.56, D.116, N.119, W.122, K.125, L.126, L.175, V.178, F.179, N.182, N.185, I.186, A.188, G.189, I.190, N.191, E.194, F.249, D.252, F.286, L.293, C.299, R.301, H.302, R.303, I.304 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:W.122, A:W.122, A:K.125, A:F.179, A:N.182, A:I.186, A:F.286, A:L.293 Hydrogen bonds: A:D.45, A:D.45, A:L.46, A:E.56, A:N.119, A:K.125, A:N.185, A:R.303, A:R.303, A:R.303, A:I.304 pi-Stacking: A:F.249 TUM.3: 31 residues within 4Å: Chain B: G.43, Q.44, D.45, L.46, N.47, E.56, D.116, N.119, W.122, K.125, L.126, L.175, V.178, F.179, N.182, N.185, I.186, A.188, G.189, I.190, N.191, E.194, F.249, D.252, F.286, L.293, C.299, R.301, H.302, R.303, I.304 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:W.122, B:W.122, B:K.125, B:L.126, B:F.179, B:N.182, B:F.286, B:F.286, B:L.293 Hydrogen bonds: B:D.45, B:L.46, B:E.56, B:N.119, B:N.119, B:N.119, B:K.125, B:N.185, B:R.303, B:R.303, B:R.303

2 x PGW: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate(Non-covalent)

PGW.2: 21 residues within 4Å: Chain A: C.107, F.110, L.111, A.114, L.118, L.120, H.124, L.127, L.128, A.131, A.132 Chain B: L.28, A.31, F.32, V.60, I.61, A.64, V.65, L.67, I.68, F.71 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:L.28, B:F.32, B:A.64, B:I.68, B:F.71, A:F.110, A:F.110, A:L.111, A:A.114 Salt bridges: A:H.124, A:H.124 PGW.4: 22 residues within 4Å: Chain A: L.28, A.31, F.32, H.35, V.60, I.61, A.64, V.65, L.67, I.68, F.71 Chain B: C.107, F.110, L.111, A.114, L.118, L.120, H.124, L.127, L.128, A.131, A.132 12 PLIP interactions: 7 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:F.110, B:L.111, B:A.114, B:L.118, B:L.128, A:F.32, A:F.32, A:I.68, A:F.71 Salt bridges: B:H.124, B:H.124 Hydrogen bonds: A:A.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoo, J. et al., GlcNAc-1-P-transferase-tunicamycin complex structure reveals basis for inhibition of N-glycosylation. Nat. Struct. Mol. Biol. (2018)

Release Date

2018-02-21

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

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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