SMTL ID : 5f84.1

Crystal structure of Drosophila Poglut1 (Rumi) complexed with its glycoprotein product (glucosylated EGF repeat) and UDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-mer

Ligands

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

UDP.1: 14 residues within 4Å: Chain A: I.188, R.217, G.218, S.219, T.221, R.225, E.263, V.264, F.266, G.280, S.284, F.285, R.286 Ligands: BGC.7 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:S.219, A:E.263, A:V.264, A:V.264, A:S.284, A:R.286 Water bridges: A:S.219, A:S.219, A:F.266, A:F.266, A:R.286, A:R.286 Salt bridges: A:R.225, A:R.225, A:R.286, A:R.286

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

SO4.2: 6 residues within 4Å: Chain A: H.184, M.194, K.197, S.265, F.266, E.267 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.266, A:E.267 Salt bridges: A:H.184, A:K.197 SO4.3: 3 residues within 4Å: Chain A: R.217, Q.242, D.262 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.217 SO4.4: 4 residues within 4Å: Chain A: R.195, R.360, M.361, K.362 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.361, A:K.362 Salt bridges: A:R.195 SO4.5: 3 residues within 4Å: Chain A: S.227, S.326, Q.327 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.327 SO4.6: 5 residues within 4Å: Chain A: G.301, D.302, E.303, K.322, S.323 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.302, A:S.323, A:S.323

1 x BGC: beta-D-glucopyranose(Post Translational Modification)

BGC.7: 12 residues within 4Å: Chain A: R.113, D.139, W.172, T.221, G.280, V.281, A.282, A.283, S.284, F.285 Chain B: S.11 Ligands: UDP.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.281, A:A.282, A:A.283, A:F.285 Water bridges: A:R.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, H. et al., Structural analysis of Notch-regulating Rumi reveals basis for pathogenic mutations. Nat. Chem. Biol. (2016)

Release Date

2016-07-20

Peptides

O-glucosyltransferase rumi: A
Coagulation factor IX: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

O-glucosyltransferase rumi

Coagulation factor IX

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