SMTL ID : 5l0r.1

human POGLUT1 in complex with Notch1 EGF12 and UDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: S.23, Q.24, N.25, S.27 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.25 Water bridges: A:Q.24, A:N.25 NAG.2: 5 residues within 4Å: Chain A: N.176, T.178, Y.180, D.205, Y.237 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.176, A:D.205, A:Y.237 Water bridges: A:N.176, A:T.178

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

UDP.3: 22 residues within 4Å: Chain A: P.143, V.145, I.148, Y.149, L.153, R.182, G.183, S.184, T.186, R.190, T.209, N.211, D.228, V.229, L.231, H.234, G.245, V.246, S.249, F.250, R.251 Ligands: GOL.4 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.149, A:S.184, A:S.184, A:T.186, A:D.228, A:V.229, A:V.229, A:L.231, A:S.249 Water bridges: A:D.105, A:V.246, A:R.251, A:R.251, B:S.9 Salt bridges: A:R.190, A:R.190, A:R.251, A:R.251

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 10 residues within 4Å: Chain A: R.79, D.105, F.122, W.136, P.143, A.248, S.249, F.250 Chain B: S.9 Ligands: UDP.3 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.105, A:S.249, A:S.249, A:F.250, B:S.9 Water bridges: A:V.246, B:S.9

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 6 residues within 4Å: Chain A: F.76, R.79, R.104, D.105 Chain B: V.4, E.6 Ligand excluded by PLIP

1 x CA: CALCIUM ION(Non-covalent)

CA.6: 7 residues within 4Å: Chain B: V.4, N.5, E.6, D.20, Q.21, G.23, E.24 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.6, B:D.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Z. et al., Structural basis of Notch O-glucosylation and O-xylosylation by mammalian protein-O-glucosyltransferase 1 (POGLUT1). Nat Commun (2017)

Release Date

2017-08-09

Peptides

Protein O-glucosyltransferase 1: A
Neurogenic locus notch homolog protein 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protein O-glucosyltransferase 1

Neurogenic locus notch homolog protein 1

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