SMTL ID : 5yyl.1

Structure of Major Royal Jelly Protein 1 Oligomer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

hetero-4-4-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: 3 residues within 4Å: Chain A: N.84, V.143, N.144 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain E: N.84, V.143, N.144 No protein-ligand interaction detected (PLIP)

8 x 94R: (3beta,14beta,17alpha)-ergosta-5,24(28)-dien-3-ol(Non-covalent)

94R.2: 12 residues within 4Å: Chain A: P.364, V.366, I.373, I.430 Chain B: F.369, F.426, I.428 Chain C: V.46, I.49 Ligands: 94R.4, 94R.5, 94R.6 11 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: B:F.369, B:F.369, B:F.426, B:I.428, C:V.46, C:I.49, A:V.366, A:I.373, A:I.430 Hydrogen bonds: A:V.366 Water bridges: A:R.375 94R.4: 10 residues within 4Å: Chain A: F.369, F.426 Chain B: P.364, V.366, I.430 Chain D: V.46, I.49 Ligands: 94R.2, 94R.5, 94R.6 8 PLIP interactions: 2 interactions with chain D, 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: D:V.46, D:I.49, B:I.430, A:F.369, A:F.369, A:F.426 Hydrogen bonds: B:V.366 Water bridges: B:R.375 94R.5: 10 residues within 4Å: Chain C: I.49, V.55 Chain D: L.45, I.49, L.64, I.67, L.71 Ligands: 94R.2, 94R.4, 94R.6 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:L.45, D:I.49, D:L.64, D:I.67, D:I.67, C:I.49, C:I.49 94R.6: 8 residues within 4Å: Chain C: L.45, L.64, I.67, L.71 Chain D: V.55 Ligands: 94R.2, 94R.4, 94R.5 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.64, C:I.67 94R.8: 12 residues within 4Å: Chain E: P.364, V.366, I.373, I.430 Chain F: F.369, F.426, I.428 Chain G: V.46, I.49 Ligands: 94R.10, 94R.11, 94R.12 11 PLIP interactions: 4 interactions with chain F, 5 interactions with chain E, 2 interactions with chain G Hydrophobic interactions: F:F.369, F:F.369, F:F.426, F:I.428, E:V.366, E:I.373, E:I.430, G:V.46, G:I.49 Hydrogen bonds: E:V.366 Water bridges: E:R.375 94R.10: 10 residues within 4Å: Chain E: F.369, F.426 Chain F: P.364, V.366, I.430 Chain H: V.46, I.49 Ligands: 94R.8, 94R.11, 94R.12 8 PLIP interactions: 3 interactions with chain F, 3 interactions with chain E, 2 interactions with chain H Hydrophobic interactions: F:I.430, E:F.369, E:F.369, E:F.426, H:V.46, H:I.49 Hydrogen bonds: F:V.366 Water bridges: F:R.375 94R.11: 10 residues within 4Å: Chain G: I.49, V.55 Chain H: L.45, I.49, L.64, I.67, L.71 Ligands: 94R.8, 94R.10, 94R.12 7 PLIP interactions: 5 interactions with chain H, 2 interactions with chain G Hydrophobic interactions: H:L.45, H:I.49, H:L.64, H:I.67, H:I.67, G:I.49, G:I.49 94R.12: 8 residues within 4Å: Chain G: L.45, L.64, I.67, L.71 Chain H: V.55 Ligands: 94R.8, 94R.10, 94R.11 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:L.64, G:I.67

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

NAG.3: 1 residues within 4Å: Chain B: N.144 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.144 NAG.9: 1 residues within 4Å: Chain F: N.144 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.144

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tian, W. et al., Architecture of the native major royal jelly protein 1 oligomer. Nat Commun (2018)

Release Date

2018-08-08

Peptides

Major royal jelly protein 1: ABEF
Apisimin: CDGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
A

F
B

C
C

D
D

G
C

H
D

Major royal jelly protein 1

Apisimin

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