SMTL ID : 2ydr.1

CpOGA D298N in complex with p53-derived O-GlcNAc peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

hetero-1-1-mer

Ligands

18 x CD: CADMIUM ION(Non-covalent)

CD.1: 3 residues within 4Å: Chain A: L.40, E.43, E.44 Ligand excluded by PLIP CD.2: 4 residues within 4Å: Chain A: E.45, E.80, D.82, D.83 Ligand excluded by PLIP CD.3: 1 residues within 4Å: Chain A: D.84 Ligand excluded by PLIP CD.4: 2 residues within 4Å: Chain A: D.89, E.117 Ligand excluded by PLIP CD.5: 2 residues within 4Å: Chain A: N.110, D.111 Ligand excluded by PLIP CD.6: 2 residues within 4Å: Chain A: D.122, D.224 Ligand excluded by PLIP CD.7: 3 residues within 4Å: Chain A: N.110, D.111, E.142 Ligand excluded by PLIP CD.8: 2 residues within 4Å: Chain A: E.244, H.248 Ligand excluded by PLIP CD.9: 2 residues within 4Å: Chain A: E.254, D.258 Ligand excluded by PLIP CD.10: 2 residues within 4Å: Chain A: E.334, D.396 Ligand excluded by PLIP CD.11: 1 residues within 4Å: Chain A: H.385 Ligand excluded by PLIP CD.12: 3 residues within 4Å: Chain A: T.372, K.376, H.405 Ligand excluded by PLIP CD.13: 3 residues within 4Å: Chain A: E.23, N.422, D.424 Ligand excluded by PLIP CD.14: 1 residues within 4Å: Chain A: E.553 Ligand excluded by PLIP CD.15: 2 residues within 4Å: Chain A: Q.12, D.30 Ligand excluded by PLIP CD.16: 2 residues within 4Å: Chain A: D.238, K.278 Ligand excluded by PLIP CD.17: 4 residues within 4Å: Chain A: D.446, R.503, E.506, N.510 Ligand excluded by PLIP CD.18: 1 residues within 4Å: Chain A: D.89 Ligand excluded by PLIP

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.19: 17 residues within 4Å: Chain A: G.159, F.160, Y.161, K.190, D.269, N.270, Y.307, T.338, V.342, W.366, N.368, V.371, D.373, Y.374, N.401 Chain B: D.5, S.6 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:D.269, A:Y.307, A:W.366 Hydrogen bonds: A:G.159, A:K.190, A:K.190, A:D.269, A:N.368, A:N.401, B:S.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schimpl, M. et al., Synergy of Peptide and Sugar in O-Glcnacase Substrate Recognition. Chem.Biol. (2012)

Release Date

2012-03-14

Peptides

O-GLCNACASE NAGJ: A
CELLULAR TUMOR ANTIGEN P53: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
P

O-GLCNACASE NAGJ

CELLULAR TUMOR ANTIGEN P53

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