SMTL ID : 5c1d.1

Human OGT in complex with UDP-5S-GlcNAc and substrate peptide (RB2L)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

1 x VAL- THR- PRO- VAL- SER- THR- ALA- ALA: Retinoblastoma-like protein 2(Non-covalent)

VAL-THR-PRO-VAL-SER-THR-ALA-ALA.1: 13 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, F.560, V.587 Ligands: 12V.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.560, A:V.587 Hydrogen bonds: A:Y.324, A:K.326 Water bridges: A:H.191, A:Q.531, A:Y.533

1 x 12V: (2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate(Non-covalent)

12V.2: 32 residues within 4Å: Chain A: H.190, H.250, P.251, T.252, H.254, L.255, L.345, G.346, P.348, F.386, F.529, N.530, Q.531, Y.533, K.534, L.558, F.560, V.587, A.588, K.590, H.593, R.596, C.609, G.611, H.612, T.613, T.614, D.617 Ligands: VAL-THR-PRO-VAL-SER-THR-ALA-ALA.1, VAL-THR-PRO-VAL-SER-THR-ALA-ALA.1, VAL-THR-PRO-VAL-SER-THR-ALA-ALA.1, VAL-THR-PRO-VAL-SER-THR-ALA-ALA.1 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:L.558 Hydrogen bonds: A:H.250, A:T.252, A:H.254, A:Q.531, A:A.588, A:A.588, A:K.590, A:H.593, A:R.596, A:H.612, A:H.612, A:H.612, A:T.613, A:T.614, A:T.614 Water bridges: A:L.345, A:Y.533, A:Y.533, A:H.593 Salt bridges: A:K.534, A:K.534 pi-Stacking: A:H.593

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 4 residues within 4Å: Chain A: I.120, H.121, S.124, N.126 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.124, A:S.124, A:S.124, A:N.126, A:N.126 Salt bridges: A:H.121 PO4.4: 5 residues within 4Å: Chain A: P.128, I.131, V.158, V.563, N.567 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.563, A:N.567

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pathak, S. et al., The active site of O-GlcNAc transferase imposes constraints on substrate sequence. Nat.Struct.Mol.Biol. (2015)

Release Date

2015-08-05

Peptides

UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit

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