SMTL ID : 3wjm.1

Crystal structure of Bombyx mori Sp2/Sp3 heterohexamer

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-3-3-mer

Ligands

1 x NAG- NAG- BMA- MAN- BMA: alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-BMA.1: 12 residues within 4Å: Chain A: E.174, K.196, Y.197, K.209, N.211, A.215, Y.686, N.689, I.690, P.691, Y.693 Chain D: F.87 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:F.87, A:K.196, A:Y.693 Hydrophobic interactions: A:Y.686

1 x NAG- NAG- BMA- BMA- MAN: beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-BMA-MAN.2: 12 residues within 4Å: Chain B: Y.206, N.208, Y.682, N.685, I.686, P.687, H.688 Chain D: F.535, P.536, K.662 Chain F: G.89, P.92 3 PLIP interactions: 1 interactions with chain F, 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: F:F.90, D:K.662 Hydrophobic interactions: B:Y.682, D:F.535

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN.3: 8 residues within 4Å: Chain C: Y.206, N.208, Y.682, N.685, I.686, P.687 Chain E: P.92 Chain F: P.540 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: C:Y.682, F:P.540

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN.4: 12 residues within 4Å: Chain A: G.89, F.90, P.92 Chain B: F.535, K.662 Chain D: N.193, Y.206, N.208, Y.682, N.685, I.686, P.687 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:K.662 Hydrophobic interactions: B:F.535, D:Y.682

1 x NAG- NAG- BMA- BMA- BMA- MAN: beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-BMA-BMA-MAN.5: 13 residues within 4Å: Chain C: G.86, F.87, P.89 Chain E: E.174, K.178, K.196, K.209, N.211, A.215, Y.686, N.689, I.690, P.691 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:Y.686 Hydrogen bonds: E:K.196

1 x NAG- NAG- BMA- MAN- BMA: beta-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-BMA.6: 12 residues within 4Å: Chain B: G.86 Chain C: F.535 Chain F: E.174, K.178, K.196, K.209, N.211, A.215, Y.686, N.689, I.690, P.691 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain F, 1 interactions with chain C Water bridges: B:F.87 Hydrogen bonds: F:K.196 Hydrophobic interactions: C:F.535

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hou, Y. et al., Crystal structure of Bombyx mori arylphorins reveals a 3:3 heterohexamer with multiple papain cleavage sites. Protein Sci. (2014)

Release Date

2014-09-24

Peptides

Arylphorin: AEF
Silkworm storage protein: BCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

F
F

B
B

C
C

D
D

Arylphorin

Silkworm storage protein