SMTL ID : 6ibo.1

Catalytic deficiency of O-GlcNAc transferase leads to X-linked intellectual disability

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

monomer

Ligands

1 x ALA- VAL- SER- ARG- ALA- ALA: ALA-VAL-SER-ARG-ALA(Non-covalent)

ALA-VAL-SER-ARG-ALA-ALA.1: 12 residues within 4Å: Chain A: H.188, H.190, H.191, H.250, P.251, Y.324, T.325, K.326, G.346, Q.531, F.560 Ligands: 12V.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.560 Hydrogen bonds: A:Y.324, A:K.326, A:G.346, A:Q.531 Water bridges: A:A.328, A:Q.531

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: 28 residues within 4Å: Chain A: H.190, P.251, T.252, H.254, L.345, G.346, P.348, F.386, F.529, N.530, Q.531, Y.533, K.534, L.558, V.587, A.588, K.590, H.593, R.596, C.609, G.611, H.612, T.613, T.614, D.617 Ligands: ALA-VAL-SER-ARG-ALA-ALA.1, ALA-VAL-SER-ARG-ALA-ALA.1, ALA-VAL-SER-ARG-ALA-ALA.1 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:L.558 Hydrogen bonds: A:T.252, A:H.254, A:L.345, 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: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: 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:N.567 Water bridges: A:N.567 PO4.4: 8 residues within 4Å: Chain A: S.487, T.492, I.495, N.496, P.506, R.507, T.508, I.510 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.487, A:S.487, A:N.496, A:R.507, A:T.508 Water bridges: A:N.496

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pravata, V.M. et al., Catalytic deficiency of O-GlcNAc transferase leads to X-linked intellectual disability. Proc.Natl.Acad.Sci.USA (2019)

Release Date

2019-07-24

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