SMTL ID : 3gwj.1

Crystal structure of Antheraea pernyi arylphorin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.43 Å

Oligo State

homo-hexamer

Ligands

6 x NAG- NAG- BMA- MAN- MAN- MAN- GLC- MAN- MAN- MAN- MAN- MAN: alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-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(Post Translational Modification)

NAG-NAG-BMA-MAN-MAN-MAN-GLC-MAN-MAN-MAN-MAN-MAN.1: 31 residues within 4Å: Chain A: K.156, N.168, A.171, E.174, Y.175, G.176, Y.187, N.189, A.193, Y.664, E.665, N.667, V.668, P.669 Chain D: L.29, Y.36, K.40, G.67, F.68, P.70, K.71, V.111, H.112, K.385 Chain E: P.518, I.519, T.520, L.521, E.522, C.642, F.643 6 PLIP interactions: 4 interactions with chain D, 1 interactions with chain A, 1 interactions with chain E Hydrogen bonds: D:Y.36, D:Y.36, D:K.40, D:V.111, A:N.168 Hydrophobic interactions: E:P.518 NAG-NAG-BMA-MAN-MAN-MAN-GLC-MAN-MAN-MAN-MAN-MAN.3: 28 residues within 4Å: Chain B: K.156, N.168, A.171, E.174, Y.175, G.176, Y.187, N.189, A.193, Y.664, E.665, N.667, V.668, P.669 Chain D: P.518, T.520, L.521, E.522, C.642 Chain F: Y.36, K.40, G.67, F.68, P.70, K.71, V.111, H.112, K.385 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:Y.36, F:Y.36, F:K.40, F:V.111, B:N.168 NAG-NAG-BMA-MAN-MAN-MAN-GLC-MAN-MAN-MAN-MAN-MAN.5: 30 residues within 4Å: Chain C: N.168, A.171, E.174, Y.175, G.176, Y.187, N.189, A.193, Y.664, E.665, N.667, V.668, P.669 Chain E: Y.36, K.40, G.67, F.68, P.70, K.71, V.111, H.112, F.383, K.385 Chain F: P.518, I.519, T.520, L.521, E.522, C.642, F.643 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:Y.36, E:K.40, E:V.111, C:N.168 NAG-NAG-BMA-MAN-MAN-MAN-GLC-MAN-MAN-MAN-MAN-MAN.7: 29 residues within 4Å: Chain A: L.29, Y.36, K.40, G.67, F.68, P.70, K.71, V.111, H.112, Y.386 Chain B: P.518, I.519, T.520, L.521, E.522, C.642 Chain D: N.168, A.171, E.174, Y.175, G.176, Y.187, N.189, A.193, Y.664, E.665, N.667, V.668, P.669 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:Y.36, A:Y.36, A:K.40, A:V.111, D:N.168 Water bridges: A:H.112 NAG-NAG-BMA-MAN-MAN-MAN-GLC-MAN-MAN-MAN-MAN-MAN.9: 28 residues within 4Å: Chain A: T.520, L.521, E.522, C.642 Chain C: L.29, Y.36, K.40, G.67, F.68, P.70, K.71, V.111, H.112, K.385, Y.386 Chain E: N.168, A.171, E.174, Y.175, G.176, Y.187, N.189, A.193, Y.664, E.665, N.667, V.668, P.669 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:Y.36, C:K.40, C:V.111, E:N.168 NAG-NAG-BMA-MAN-MAN-MAN-GLC-MAN-MAN-MAN-MAN-MAN.11: 29 residues within 4Å: Chain B: Y.36, K.40, G.67, F.68, P.70, K.71, V.111, H.112, K.385, Y.386 Chain C: P.518, T.520, L.521, E.522, C.642, F.643 Chain F: N.168, A.171, E.174, Y.175, G.176, Y.187, N.189, A.193, Y.664, E.665, N.667, V.668, P.669 8 PLIP interactions: 3 interactions with chain F, 4 interactions with chain B, 1 interactions with chain C Hydrogen bonds: F:N.168, B:Y.36, B:K.40, B:V.111 Water bridges: F:E.170, F:E.170, B:H.112 Hydrophobic interactions: C:P.518

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

NAG-NAG.2: 3 residues within 4Å: Chain A: Y.335, N.337 Chain C: G.331 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: G.331 Chain B: Y.335, N.337 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: G.331 Chain C: Y.335, N.337 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain D: N.337 Chain F: G.357 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:G.357 NAG-NAG.10: 2 residues within 4Å: Chain E: Y.335, N.337 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain F: Y.335, N.337 No protein-ligand interaction detected (PLIP)

6 x FMT: FORMIC ACID(Non-functional Binders)

FMT.13: 5 residues within 4Å: Chain A: Y.272, H.300, Y.305, R.309 Chain B: S.270 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.300, A:R.309 Water bridges: B:W.271 FMT.14: 5 residues within 4Å: Chain B: Y.272, H.300, Y.305, R.309 Chain C: S.270 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Water bridges: C:W.271, C:R.411 Hydrogen bonds: B:Y.305, B:R.309 FMT.15: 4 residues within 4Å: Chain A: S.270 Chain C: H.300, Y.305, R.309 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Water bridges: A:W.271, A:R.411 Hydrogen bonds: C:H.300, C:R.309 FMT.16: 5 residues within 4Å: Chain D: Y.272, H.300, Y.305, R.309 Chain E: S.270 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:H.300, D:R.309 Water bridges: E:W.271, E:R.411 FMT.17: 5 residues within 4Å: Chain E: Y.272, H.300, Y.305, R.309 Chain F: S.270 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain E Water bridges: F:W.271, F:R.411 Hydrogen bonds: E:R.309, E:R.309 FMT.18: 5 residues within 4Å: Chain D: S.270 Chain F: Y.272, H.300, Y.305, R.309 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain D Hydrogen bonds: F:H.300, F:R.309 Water bridges: D:W.271, D:R.411

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ryu, K.S. et al., The presence of monoglucosylated N196-glycan is important for the structural stability of storage protein, arylphorin. Biochem.J. (2009)

Release Date

2009-05-05

Peptides

Arylphorin: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Arylphorin