SMTL ID : 5vif.1

Electrophilic probes for deciphering substrate recognition by O-GlcNAc transferase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 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, F.529, 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: 9C1.2 21 PLIP interactions: 20 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.558, A:F.560 Hydrogen bonds: A:H.254, A:N.530, 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.614, B:S.9 Water bridges: A:Y.533, A:K.590, A:H.593 Salt bridges: A:K.534, A:K.534, A:H.612 pi-Stacking: A:H.593 UDP.3: 22 residues within 4Å: Chain C: P.251, F.529, 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: 9C1.4 19 PLIP interactions: 18 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:L.558, C:F.560 Hydrogen bonds: C:N.530, 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.614, D:S.9 Water bridges: C:K.590 Salt bridges: C:K.534, C:K.534, C:H.612 pi-Stacking: C:H.593

2 x 9C1: 2-{[(2E)-4-chlorobut-2-enoyl]amino}-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

9C1.2: 16 residues within 4Å: Chain A: H.190, M.193, H.250, 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 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.252, A:L.345, A:H.612, A:T.613 Water bridges: A:L.345, A:Y.533, A:Y.533 9C1.4: 16 residues within 4Å: Chain C: H.190, M.193, H.250, 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.3 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.252, C:T.252, C:L.345, C:H.612, C:T.613 Water bridges: C:L.345

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hu, C.W. et al., Electrophilic probes for deciphering substrate recognition by O-GlcNAc transferase. Nat. Chem. Biol. (2017)

Release Date

2017-10-18

Peptides

UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit: AC
CKII: 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

CKII

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