SMTL ID : 4gz5.5 (4 other biounits)

Crystal structure of human O-GlcNAc Transferase with UDP-GlcNAc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.08 Å

Oligo State

homo-12-mer

Ligands

12 x UD1: URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE(Non-covalent)

UD1.1: 25 residues within 4Å: Chain A: H.190, M.193, P.251, T.252, L.255, L.345, G.346, P.348, F.386, Q.531, Y.533, K.534, L.558, V.587, A.588, P.589, K.590, H.593, R.596, C.609, H.612, T.613, T.614, D.617 Chain C: C.5 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:L.558 Hydrogen bonds: A:T.252, 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:T.613, A:T.613, A:T.613, A:T.614 Salt bridges: A:K.534, A:K.534, A:H.612 pi-Stacking: A:H.593 UD1.6: 25 residues within 4Å: Chain A: C.5 Chain B: H.190, M.193, P.251, T.252, L.255, L.345, G.346, P.348, F.386, Q.531, Y.533, K.534, L.558, V.587, A.588, P.589, K.590, H.593, R.596, C.609, H.612, T.613, T.614, D.617 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:L.558 Hydrogen bonds: B:T.252, B:L.345, B:Q.531, B:A.588, B:A.588, B:K.590, B:H.593, B:R.596, B:H.612, B:H.612, B:T.613, B:T.613, B:T.613, B:T.614 Salt bridges: B:K.534, B:K.534, B:H.612 pi-Stacking: B:H.593 UD1.11: 25 residues within 4Å: Chain B: C.5 Chain C: H.190, M.193, P.251, T.252, L.255, L.345, G.346, P.348, F.386, Q.531, Y.533, K.534, L.558, V.587, A.588, P.589, K.590, H.593, R.596, C.609, H.612, T.613, T.614, D.617 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:L.558 Hydrogen bonds: C:T.252, C:L.345, C:Q.531, C:A.588, C:A.588, C:K.590, C:H.593, C:R.596, C:H.612, C:H.612, C:T.613, C:T.613, C:T.613, C:T.614 Salt bridges: C:K.534, C:K.534, C:H.612 pi-Stacking: C:H.593 UD1.16: 28 residues within 4Å: Chain D: H.190, M.193, H.250, P.251, T.252, H.254, L.255, L.345, G.346, P.348, F.386, F.529, Q.531, Y.533, K.534, L.558, F.560, V.587, A.588, K.590, H.593, R.596, C.609, H.612, T.613, T.614, D.617 Chain E: C.5 24 PLIP interactions: 24 interactions with chain D Hydrophobic interactions: D:L.558, D:F.560 Hydrogen bonds: D:T.252, D:H.254, D:L.345, D:Q.531, D:A.588, D:A.588, D:K.590, D:H.593, D:R.596, D:H.612, D:H.612, D:H.612, D:T.613, D:T.613, D:T.613, D:T.614 Water bridges: D:Y.533, D:Y.533 Salt bridges: D:K.534, D:K.534, D:H.612 pi-Stacking: D:H.593 UD1.21: 25 residues within 4Å: Chain E: H.190, M.193, P.251, T.252, L.255, L.345, G.346, P.348, F.386, F.529, Q.531, Y.533, K.534, L.558, V.587, A.588, K.590, H.593, R.596, C.609, H.612, T.613, T.614, D.617 Chain F: C.5 20 PLIP interactions: 20 interactions with chain E Hydrophobic interactions: E:L.558 Hydrogen bonds: E:T.252, E:H.254, E:L.345, E:Q.531, E:A.588, E:A.588, E:K.590, E:H.593, E:H.612, E:H.612, E:T.613, E:T.613, E:T.613, E:T.614, E:T.614 Salt bridges: E:K.534, E:K.534, E:H.612 pi-Stacking: E:H.593 UD1.26: 26 residues within 4Å: Chain D: C.5 Chain F: H.190, M.193, H.250, P.251, T.252, L.255, L.345, G.346, P.348, F.386, F.529, Q.531, Y.533, K.534, L.558, V.587, A.588, K.590, H.593, R.596, C.609, H.612, T.613, T.614, D.617 24 PLIP interactions: 24 interactions with chain F Hydrophobic interactions: F:L.558 Hydrogen bonds: F:T.252, F:H.254, F:L.345, F:Q.531, F:Y.533, F:A.588, F:A.588, F:K.590, F:K.590, F:H.593, F:R.596, F:H.612, F:H.612, F:H.612, F:T.613, F:T.613, F:T.613, F:T.614, F:T.614 Salt bridges: F:K.534, F:K.534, F:H.612 pi-Stacking: F:H.593 UD1.31: 28 residues within 4Å: Chain G: H.190, M.193, H.250, P.251, T.252, H.254, L.255, L.345, G.346, P.348, F.386, F.529, Q.531, Y.533, K.534, L.558, F.560, V.587, A.588, K.590, H.593, R.596, C.609, H.612, T.613, T.614, D.617 Chain H: C.5 24 PLIP interactions: 24 interactions with chain G Hydrophobic interactions: G:L.558, G:F.560 Hydrogen bonds: G:T.252, G:H.254, G:L.345, G:Q.531, G:A.588, G:A.588, G:K.590, G:H.593, G:R.596, G:H.612, G:H.612, G:H.612, G:T.613, G:T.613, G:T.613, G:T.614 Water bridges: G:Y.533, G:Y.533 Salt bridges: G:K.534, G:K.534, G:H.612 pi-Stacking: G:H.593 UD1.36: 25 residues within 4Å: Chain H: H.190, M.193, P.251, T.252, L.255, L.345, G.346, P.348, F.386, F.529, Q.531, Y.533, K.534, L.558, V.587, A.588, K.590, H.593, R.596, C.609, H.612, T.613, T.614, D.617 Chain I: C.5 20 PLIP interactions: 20 interactions with chain H Hydrophobic interactions: H:L.558 Hydrogen bonds: H:T.252, H:H.254, H:L.345, H:Q.531, H:A.588, H:A.588, H:K.590, H:H.593, H:H.612, H:H.612, H:T.613, H:T.613, H:T.613, H:T.614, H:T.614 Salt bridges: H:K.534, H:K.534, H:H.612 pi-Stacking: H:H.593 UD1.41: 26 residues within 4Å: Chain G: C.5 Chain I: H.190, M.193, H.250, P.251, T.252, L.255, L.345, G.346, P.348, F.386, F.529, Q.531, Y.533, K.534, L.558, V.587, A.588, K.590, H.593, R.596, C.609, H.612, T.613, T.614, D.617 24 PLIP interactions: 24 interactions with chain I Hydrophobic interactions: I:L.558 Hydrogen bonds: I:T.252, I:H.254, I:L.345, I:Q.531, I:Y.533, I:A.588, I:A.588, I:K.590, I:K.590, I:H.593, I:R.596, I:H.612, I:H.612, I:H.612, I:T.613, I:T.613, I:T.613, I:T.614, I:T.614 Salt bridges: I:K.534, I:K.534, I:H.612 pi-Stacking: I:H.593 UD1.46: 28 residues within 4Å: Chain J: H.190, M.193, H.250, P.251, T.252, H.254, L.255, L.345, G.346, P.348, F.386, F.529, Q.531, Y.533, K.534, L.558, F.560, V.587, A.588, K.590, H.593, R.596, C.609, H.612, T.613, T.614, D.617 Chain K: C.5 24 PLIP interactions: 24 interactions with chain J Hydrophobic interactions: J:L.558, J:F.560 Hydrogen bonds: J:T.252, J:H.254, J:L.345, J:Q.531, J:A.588, J:A.588, J:K.590, J:H.593, J:R.596, J:H.612, J:H.612, J:H.612, J:T.613, J:T.613, J:T.613, J:T.614 Water bridges: J:Y.533, J:Y.533 Salt bridges: J:K.534, J:K.534, J:H.612 pi-Stacking: J:H.593 UD1.51: 25 residues within 4Å: Chain K: H.190, M.193, P.251, T.252, L.255, L.345, G.346, P.348, F.386, F.529, Q.531, Y.533, K.534, L.558, V.587, A.588, K.590, H.593, R.596, C.609, H.612, T.613, T.614, D.617 Chain L: C.5 20 PLIP interactions: 20 interactions with chain K Hydrophobic interactions: K:L.558 Hydrogen bonds: K:T.252, K:H.254, K:L.345, K:Q.531, K:A.588, K:A.588, K:K.590, K:H.593, K:H.612, K:H.612, K:T.613, K:T.613, K:T.613, K:T.614, K:T.614 Salt bridges: K:K.534, K:K.534, K:H.612 pi-Stacking: K:H.593 UD1.56: 26 residues within 4Å: Chain J: C.5 Chain L: H.190, M.193, H.250, P.251, T.252, L.255, L.345, G.346, P.348, F.386, F.529, Q.531, Y.533, K.534, L.558, V.587, A.588, K.590, H.593, R.596, C.609, H.612, T.613, T.614, D.617 24 PLIP interactions: 24 interactions with chain L Hydrophobic interactions: L:L.558 Hydrogen bonds: L:T.252, L:H.254, L:L.345, L:Q.531, L:Y.533, L:A.588, L:A.588, L:K.590, L:K.590, L:H.593, L:R.596, L:H.612, L:H.612, L:H.612, L:T.613, L:T.613, L:T.613, L:T.614, L:T.614 Salt bridges: L:K.534, L:K.534, L:H.612 pi-Stacking: L:H.593

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

SO4.2: 5 residues within 4Å: Chain A: N.13, N.14, N.17, A.44, N.48 Ligand excluded by PLIP SO4.3: 4 residues within 4Å: Chain A: Y.517, R.559, F.584, P.586 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: M.628, N.654, R.655 Ligand excluded by PLIP SO4.5: 5 residues within 4Å: Chain A: G.57, K.58, L.59, Q.60, E.61 Ligand excluded by PLIP SO4.7: 5 residues within 4Å: Chain B: N.13, N.14, N.17, A.44, N.48 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain B: Y.517, R.559, F.584, P.586 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain B: M.628, N.654, R.655 Ligand excluded by PLIP SO4.10: 5 residues within 4Å: Chain B: G.57, K.58, L.59, Q.60, E.61 Ligand excluded by PLIP SO4.12: 5 residues within 4Å: Chain C: N.13, N.14, N.17, A.44, N.48 Ligand excluded by PLIP SO4.13: 4 residues within 4Å: Chain C: Y.517, R.559, F.584, P.586 Ligand excluded by PLIP SO4.14: 3 residues within 4Å: Chain C: M.628, N.654, R.655 Ligand excluded by PLIP SO4.15: 5 residues within 4Å: Chain C: G.57, K.58, L.59, Q.60, E.61 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain D: N.13, N.17, A.44, N.48 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain D: R.559, F.584, S.585 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain D: M.628, N.654, R.655 Ligand excluded by PLIP SO4.20: 4 residues within 4Å: Chain D: K.58, L.59, Q.60, E.61 Ligand excluded by PLIP SO4.22: 4 residues within 4Å: Chain E: N.13, N.17, A.44, N.48 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain E: R.559, F.584, P.586 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain E: M.628, N.654, R.655 Ligand excluded by PLIP SO4.25: 4 residues within 4Å: Chain E: K.58, L.59, Q.60, E.61 Ligand excluded by PLIP SO4.27: 4 residues within 4Å: Chain F: N.13, N.17, A.44, N.48 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain F: R.559, F.584, P.586 Ligand excluded by PLIP SO4.29: 3 residues within 4Å: Chain F: M.628, N.654, R.655 Ligand excluded by PLIP SO4.30: 5 residues within 4Å: Chain F: G.57, K.58, L.59, Q.60, E.61 Ligand excluded by PLIP SO4.32: 4 residues within 4Å: Chain G: N.13, N.17, A.44, N.48 Ligand excluded by PLIP SO4.33: 3 residues within 4Å: Chain G: R.559, F.584, S.585 Ligand excluded by PLIP SO4.34: 3 residues within 4Å: Chain G: M.628, N.654, R.655 Ligand excluded by PLIP SO4.35: 4 residues within 4Å: Chain G: K.58, L.59, Q.60, E.61 Ligand excluded by PLIP SO4.37: 4 residues within 4Å: Chain H: N.13, N.17, A.44, N.48 Ligand excluded by PLIP SO4.38: 3 residues within 4Å: Chain H: R.559, F.584, P.586 Ligand excluded by PLIP SO4.39: 3 residues within 4Å: Chain H: M.628, N.654, R.655 Ligand excluded by PLIP SO4.40: 4 residues within 4Å: Chain H: K.58, L.59, Q.60, E.61 Ligand excluded by PLIP SO4.42: 4 residues within 4Å: Chain I: N.13, N.17, A.44, N.48 Ligand excluded by PLIP SO4.43: 3 residues within 4Å: Chain I: R.559, F.584, P.586 Ligand excluded by PLIP SO4.44: 3 residues within 4Å: Chain I: M.628, N.654, R.655 Ligand excluded by PLIP SO4.45: 5 residues within 4Å: Chain I: G.57, K.58, L.59, Q.60, E.61 Ligand excluded by PLIP SO4.47: 4 residues within 4Å: Chain J: N.13, N.17, A.44, N.48 Ligand excluded by PLIP SO4.48: 3 residues within 4Å: Chain J: R.559, F.584, S.585 Ligand excluded by PLIP SO4.49: 3 residues within 4Å: Chain J: M.628, N.654, R.655 Ligand excluded by PLIP SO4.50: 4 residues within 4Å: Chain J: K.58, L.59, Q.60, E.61 Ligand excluded by PLIP SO4.52: 4 residues within 4Å: Chain K: N.13, N.17, A.44, N.48 Ligand excluded by PLIP SO4.53: 3 residues within 4Å: Chain K: R.559, F.584, P.586 Ligand excluded by PLIP SO4.54: 3 residues within 4Å: Chain K: M.628, N.654, R.655 Ligand excluded by PLIP SO4.55: 4 residues within 4Å: Chain K: K.58, L.59, Q.60, E.61 Ligand excluded by PLIP SO4.57: 4 residues within 4Å: Chain L: N.13, N.17, A.44, N.48 Ligand excluded by PLIP SO4.58: 3 residues within 4Å: Chain L: R.559, F.584, P.586 Ligand excluded by PLIP SO4.59: 3 residues within 4Å: Chain L: M.628, N.654, R.655 Ligand excluded by PLIP SO4.60: 5 residues within 4Å: Chain L: G.57, K.58, L.59, Q.60, E.61 Ligand excluded by PLIP

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: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
D

C
D

D
A

E
B

F
C

G
A

H
B

I
C

J
A

K
B

L
C

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

Related Entries With Identical Sequence