SMTL ID : 5uk5.1

Complex of Notch1(EGF8-12) bound to Jagged1(N-EGF3)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.51 Å

Oligo State

hetero-1-1-mer

Ligands

1 x BGC- XYS: alpha-D-xylopyranose-(1-3)-beta-D-glucopyranose(Post Translational Modification)

BGC-XYS.1: 6 residues within 4Å: Chain A: E.163, S.166, P.168, G.180, E.181, F.182 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.180 Water bridges: A:F.182

3 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: N.43, I.44, D.46, D.60, R.61, A.63 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:I.44, A:D.46, A:D.60, A:R.61, H2O.1 CA.3: 7 residues within 4Å: Chain A: D.120, V.121, E.123, N.139, T.140, G.142, S.143 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.120, A:V.121, A:E.123, A:T.140, A:S.143 CA.4: 5 residues within 4Å: Chain A: D.160, V.161, E.163, D.177, Q.178 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.160, A:E.163, A:D.177, H2O.1, H2O.1

3 x FUC: alpha-L-fucopyranose(Post Translational Modification)

FUC.5: 7 residues within 4Å: Chain A: G.17, T.19, V.30, C.31 Chain B: N.271, G.274, N.287 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.271, B:G.274 Hydrophobic interactions: A:V.30 FUC.9: 8 residues within 4Å: Chain A: D.172, T.174, I.185, C.186, M.187 Chain B: E.54, Y.55, Q.56 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.174 Water bridges: B:Y.55 FUC.11: 5 residues within 4Å: Chain A: H.21 Chain B: R.282, T.284, S.296, P.298 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.21 Hydrophobic interactions: B:P.298

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

BGC.6: 3 residues within 4Å: Chain A: A.83, S.86, P.88 No protein-ligand interaction detected (PLIP) BGC.7: 2 residues within 4Å: Chain A: S.143, F.144 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.156

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

NAG.8: 2 residues within 4Å: Chain A: T.153, G.154 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.154 NAG.10: 1 residues within 4Å: Chain B: N.190 No protein-ligand interaction detected (PLIP)

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.12: 2 residues within 4Å: Chain B: H.163, R.174 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.174, B:R.174

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Luca, V.C. et al., Notch-Jagged complex structure implicates a catch bond in tuning ligand sensitivity. Science (2017)

Release Date

2017-03-08

Peptides

Neurogenic locus notch homolog protein 1: A
Protein jagged-1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Neurogenic locus notch homolog protein 1

Protein jagged-1