SMTL ID : 4xl1.3 (2 other biounits)

Complex of Notch1 (EGF11-13) bound to Delta-like 4 (N-EGF1)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-2-2-mer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 4 residues within 4Å: Chain B: E.135, N.137 Chain D: N.137, N.138 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain B: N.137, N.138 Chain D: E.135, N.137, R.142 No protein-ligand interaction detected (PLIP)

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

BGC.3: 4 residues within 4Å: Chain A: E.5, S.25, F.26 Chain B: D.194 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:F.26, B:D.194 Water bridges: A:R.38 BGC.4: 4 residues within 4Å: Chain A: E.45, S.48, F.64, Y.76 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.45, A:E.45, A:S.48 BGC.6: 3 residues within 4Å: Chain A: E.83, S.86, P.88 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.83, A:S.86 BGC.12: 4 residues within 4Å: Chain C: S.25, F.26 Chain D: D.194, Q.195 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:D.194, D:Q.195 Water bridges: C:R.38 BGC.13: 4 residues within 4Å: Chain C: E.45, S.48, P.50, F.64 No protein-ligand interaction detected (PLIP) BGC.15: 3 residues within 4Å: Chain C: E.83, S.86, F.102 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.83, C:S.86

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

FUC.5: 9 residues within 4Å: Chain A: D.54, T.56, I.67, C.68, M.69 Chain B: H.40, Y.41, Q.42, T.90 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.90, B:T.90 Water bridges: B:Y.41 FUC.14: 8 residues within 4Å: Chain C: D.54, T.56, I.67, C.68, M.69 Chain D: H.40, Y.41, Q.42 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.90, D:T.90 Water bridges: D:Y.41, D:A.43

6 x CA: CALCIUM ION(Non-covalent)

CA.7: 5 residues within 4Å: Chain A: D.42, V.43, E.45, D.59, Q.60 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.42, A:D.59, A:D.59, A:Q.60, H2O.2 CA.8: 5 residues within 4Å: Chain A: N.80, T.81, E.83, D.97, K.98 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.81, A:D.97, A:K.98, H2O.1, H2O.2 CA.9: 6 residues within 4Å: Chain A: E.5, N.21, T.22, L.23, G.24, S.25 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.5, A:T.22, A:S.25, H2O.3 CA.16: 5 residues within 4Å: Chain C: N.80, T.81, E.83, D.97, K.98 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:T.81, C:E.83, C:D.97, C:K.98, H2O.8 CA.17: 5 residues within 4Å: Chain C: D.42, V.43, E.45, D.59, Q.60 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.42, C:V.43, C:Q.60, H2O.8, H2O.8 CA.18: 8 residues within 4Å: Chain C: D.2, V.3, E.5, N.21, T.22, L.23, G.24, S.25 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.2, C:D.2, C:E.5, C:T.22, C:S.25

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

NAG.10: 4 residues within 4Å: Chain B: P.49, C.50, N.54 Chain C: E.101 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:C.50, B:N.54, C:E.101, C:E.101 NAG.11: 5 residues within 4Å: Chain A: I.61 Chain B: N.84 Chain C: S.111, G.112, S.117 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.117, C:S.117 NAG.19: 4 residues within 4Å: Chain A: E.101 Chain D: P.49, C.50, N.54 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:C.50, D:N.54, A:E.101 NAG.20: 2 residues within 4Å: Chain D: G.1, N.84 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Luca, V.C. et al., Structural biology. Structural basis for Notch1 engagement of Delta-like 4. Science (2015)

Release Date

2015-03-04

Peptides

Neurogenic locus notch homolog protein 1: AC
Delta-like protein: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
D

B
B

D
E

Neurogenic locus notch homolog protein 1

Delta-like protein

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