SMTL ID : 4cdr.2 (3 other biounits)

Human O-GlcNAc transferase in complex with a bisubstrate inhibitor, Goblin1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.15 Å

Oligo State

monomer

Ligands

1 x ACE- VAL- THR- PRO- VAL- SRZ- THR- ALA- NH2: GOBLIN1(Non-covalent)

ACE-VAL-THR-PRO-VAL-SRZ-THR-ALA-NH2.1: 15 residues within 4Å: Chain A: H.188, H.190, H.191, N.249, H.250, P.251, Y.324, T.325, K.326, Q.531, V.587, H.612, T.613 Ligands: SO4.3, UDP.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.587, A:H.612 Hydrogen bonds: A:Y.324, A:K.326

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: N.13, N.17, A.44, N.48 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.13, A:N.17, A:N.48 SO4.3: 5 residues within 4Å: Chain A: K.122, H.153, H.191 Ligands: ACE-VAL-THR-PRO-VAL-SRZ-THR-ALA-NH2.1, ACE-VAL-THR-PRO-VAL-SRZ-THR-ALA-NH2.1 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.122, A:H.153, A:H.191 SO4.4: 4 residues within 4Å: Chain A: F.294, I.295, D.296, R.309 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.294, A:D.296 Salt bridges: A:R.309 SO4.5: 1 residues within 4Å: Chain A: H.293 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.293 SO4.6: 2 residues within 4Å: Chain A: R.183, L.184 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.184 Salt bridges: A:R.183 SO4.7: 2 residues within 4Å: Chain A: N.654, R.655 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.655, A:Q.656 Salt bridges: A:R.655

1 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.8: 19 residues within 4Å: Chain A: P.251, H.254, Q.531, K.534, L.558, F.560, V.587, A.588, K.590, H.593, R.596, H.612, T.613, T.614, D.617 Ligands: ACE-VAL-THR-PRO-VAL-SRZ-THR-ALA-NH2.1, ACE-VAL-THR-PRO-VAL-SRZ-THR-ALA-NH2.1, ACE-VAL-THR-PRO-VAL-SRZ-THR-ALA-NH2.1, ACE-VAL-THR-PRO-VAL-SRZ-THR-ALA-NH2.1 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.558 Hydrogen bonds: A:H.254, A:Q.531, A:A.588, A:A.588, A:K.590, A:K.590, A:H.593, A:H.612, A:T.613, A:T.613, A:T.614, A:T.614 Salt bridges: A:K.534, A:K.534 pi-Stacking: A:H.593

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Borodkin, V.S. et al., Bisubstrate Udp-Peptide Conjugates as Human O-Glcnac Transferase Inhibitors. Biochem.J. (2014)

Release Date

2013-12-04

Peptides

UDP-N-ACETYLGLUCOSAMINE--PEPTIDE N-ACETYLGLUCOSAMINYLTRANSFERASE 110 KDA SUBUNIT: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

UDP-N-ACETYLGLUCOSAMINE--PEPTIDE N-ACETYLGLUCOSAMINYLTRANSFERASE 110 KDA SUBUNIT

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