SMTL ID : 4gyw.4 (3 other biounits)

Crystal structure of human O-GlcNAc Transferase in complex with UDP and a glycopeptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-2-2-mer

Ligands

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

UDP.1: 22 residues within 4Å: Chain A: P.251, H.254, N.530, Q.531, K.534, L.558, F.560, V.587, A.588, K.590, H.593, R.596, G.611, H.612, T.613, T.614, D.617 Chain B: T.6, P.7, V.8, S.9 Ligands: NAG.3 22 PLIP interactions: 21 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.558, A:F.560 Hydrogen bonds: 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:T.613, A:T.613, A:T.614, A:T.614, B:S.9 Water bridges: A:N.530, A:Q.531, A:H.593 Salt bridges: A:K.534, A:K.534, A:H.612 pi-Stacking: A:H.593 UDP.5: 22 residues within 4Å: Chain C: P.251, H.254, N.530, Q.531, K.534, L.558, F.560, V.587, A.588, K.590, H.593, R.596, G.611, H.612, T.613, T.614, D.617 Chain D: T.6, P.7, V.8, S.9 Ligands: NAG.7 22 PLIP interactions: 1 interactions with chain D, 21 interactions with chain C Hydrogen bonds: D:S.9, C:Q.531, C:A.588, C:A.588, C:K.590, C:H.593, C:R.596, C:H.612, C:T.613, C:T.613, C:T.613, C:T.614 Hydrophobic interactions: C:L.558, C:F.560 Water bridges: C:Q.531, C:Y.533, C:Y.533, C:T.614 Salt bridges: C:K.534, C:K.534, C:H.612 pi-Stacking: C:H.593

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

SO4.2: 3 residues within 4Å: Chain A: G.57, L.59, Q.60 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.57, A:L.59, A:Q.60, A:Q.60 Water bridges: A:E.61 SO4.4: 5 residues within 4Å: Chain A: K.326, G.327, A.328 Chain B: N.12, M.13 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:M.13, A:G.327, A:A.328 Water bridges: B:N.12 Salt bridges: A:K.326 SO4.6: 3 residues within 4Å: Chain C: G.57, L.59, Q.60 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.57, C:L.59, C:Q.60, C:Q.60 Water bridges: C:E.61 SO4.8: 5 residues within 4Å: Chain C: K.326, G.327, A.328 Chain D: N.12, M.13 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:G.327, C:A.328, D:M.13 Salt bridges: C:K.326 Water bridges: D:N.12

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 15 residues within 4Å: Chain A: H.190, M.193, P.251, T.252, L.255, L.345, G.346, P.348, F.386, Y.533, C.609, H.612, T.613 Chain B: S.9 Ligands: UDP.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.252, A:H.612 Water bridges: A:L.345 NAG.7: 15 residues within 4Å: Chain C: H.190, M.193, P.251, T.252, L.255, L.345, G.346, P.348, F.386, Y.533, C.609, H.612, T.613 Chain D: S.9 Ligands: UDP.5 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.252, C:H.612 Water bridges: C:L.345

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lazarus, M.B. et al., Structural snapshots of the reaction coordinate for O-GlcNAc transferase. Nat.Chem.Biol. (2012)

Release Date

2012-10-31

Peptides

UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit: AC
Casein kinase II subunit alpha: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

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

Casein kinase II subunit alpha

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