SMTL ID : 9b3n.1

Human Notch-1 EGFs 20-24

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

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

BGC-XYP.1: 6 residues within 4Å: Chain A: E.42, S.45, P.47, A.59, G.60, Y.61 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.42, A:A.59

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

BGC.2: 4 residues within 4Å: Chain A: E.4, S.7, P.9, Y.23 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.4, A:E.4, A:E.4 Water bridges: A:Y.23

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

FUC.3: 5 residues within 4Å: Chain A: G.13, T.15, T.26, C.27, R.28 No protein-ligand interaction detected (PLIP) FUC.4: 5 residues within 4Å: Chain A: S.169, D.180, C.181, L.182 Ligands: EDO.11 No protein-ligand interaction detected (PLIP) FUC.5: 5 residues within 4Å: Chain A: Q.51, T.53, N.64, C.65, L.66 No protein-ligand interaction detected (PLIP) FUC.6: 4 residues within 4Å: Chain A: G.129, S.131, H.142, Q.144 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:H.142 Hydrogen bonds: A:G.129

4 x CA: CALCIUM ION(Non-covalent)

CA.7: 5 residues within 4Å: Chain A: D.155, I.156, D.158, D.172, G.173 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.155, A:I.156, A:D.172, A:G.173, H2O.2 CA.8: 5 residues within 4Å: Chain A: N.39, I.40, E.42, D.56, D.57 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:I.40, A:E.42, A:D.56, A:D.57, H2O.2 CA.9: 7 residues within 4Å: Chain A: D.117, I.118, E.120, N.134, T.135, G.137, G.138 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.117, A:I.118, A:T.135, A:G.138, H2O.2 CA.10: 3 residues within 4Å: Chain A: N.3, D.18, M.19 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.18, A:D.18, A:M.19

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.11: 5 residues within 4Å: Chain A: N.162, G.167, G.168, S.169 Ligands: FUC.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.169 Water bridges: A:N.162, A:N.162, A:C.170 EDO.12: 4 residues within 4Å: Chain A: I.156, D.157, D.158, R.160 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.158, A:D.158 Water bridges: A:P.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bo, Z. et al., Structural and functional studies of the EGF20-27 region reveal new features of the human Notch receptor important for optimal activation. Structure (2024)

Release Date

2024-10-16

Peptides

Neurogenic locus notch homolog protein 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Neurogenic locus notch homolog protein 1