SMTL ID : 4l37.1

SP2-SP3 - a complex of two storage proteins from Bombyx mori hemolymph

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-3-3-mer

Ligands

6 x NAG- NAG- BMA- MAN- MAN: alpha-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(Non-functional Binders)

NAG-NAG-BMA-MAN-MAN.1: 9 residues within 4Å: Chain A: K.159, N.177, Y.190, N.192, Y.666, N.669, I.670, P.671 Chain D: P.524 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:Y.666, D:P.524 Hydrogen bonds: A:N.177 NAG-NAG-BMA-MAN-MAN.2: 15 residues within 4Å: Chain A: G.70, F.71, P.73 Chain B: E.158, K.180, Y.181, K.193, N.195, A.199, Y.670, N.673, P.675 Chain E: F.519, P.520, K.646 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain B Hydrophobic interactions: E:F.519, B:Y.670 Hydrogen bonds: B:K.180 NAG-NAG-BMA-MAN-MAN.13: 9 residues within 4Å: Chain C: K.159, N.177, Y.190, N.192, Y.666, N.669, I.670, P.671 Chain F: P.524 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: C:Y.666, F:P.524 Hydrogen bonds: C:N.177 NAG-NAG-BMA-MAN-MAN.14: 15 residues within 4Å: Chain A: F.519, P.520, K.646 Chain C: G.70, F.71, P.73 Chain D: E.158, K.180, Y.181, K.193, N.195, A.199, Y.670, N.673, P.675 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:Y.670, A:F.519 Hydrogen bonds: D:K.180 NAG-NAG-BMA-MAN-MAN.25: 9 residues within 4Å: Chain B: P.524 Chain E: K.159, N.177, Y.190, N.192, Y.666, N.669, I.670, P.671 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain B Hydrophobic interactions: E:Y.666, B:P.524 Hydrogen bonds: E:N.177 NAG-NAG-BMA-MAN-MAN.26: 15 residues within 4Å: Chain C: F.519, P.520, K.646 Chain E: G.70, F.71, P.73 Chain F: E.158, K.180, Y.181, K.193, N.195, A.199, Y.670, N.673, P.675 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain F Hydrophobic interactions: C:F.519, F:Y.670 Hydrogen bonds: F:K.180

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 6 residues within 4Å: Chain A: S.273 Chain C: Y.275, H.303, Y.308, I.311, R.312 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Water bridges: A:D.315, A:R.414 Hydrogen bonds: C:Y.275 Salt bridges: C:H.303, C:R.312 SO4.9: 8 residues within 4Å: Chain B: S.276, W.277, R.417 Chain F: Y.278, H.306, Y.311, V.314, R.315 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain B Hydrogen bonds: F:Y.311, B:W.277, B:R.417 Salt bridges: F:H.306, F:R.315 SO4.15: 6 residues within 4Å: Chain C: S.273 Chain E: Y.275, H.303, Y.308, I.311, R.312 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain E Water bridges: C:D.315, C:R.414 Hydrogen bonds: E:Y.275 Salt bridges: E:H.303, E:R.312 SO4.21: 8 residues within 4Å: Chain B: Y.278, H.306, Y.311, V.314, R.315 Chain D: S.276, W.277, R.417 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:W.277, D:R.417, B:Y.311 Salt bridges: B:H.306, B:R.315 SO4.27: 6 residues within 4Å: Chain A: Y.275, H.303, Y.308, I.311, R.312 Chain E: S.273 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:Y.275 Salt bridges: A:H.303, A:R.312 Water bridges: E:D.315, E:R.414 SO4.33: 8 residues within 4Å: Chain D: Y.278, H.306, Y.311, V.314, R.315 Chain F: S.276, W.277, R.417 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain F Hydrogen bonds: D:Y.311, F:W.277, F:R.417 Salt bridges: D:H.306, D:R.315

9 x NA: SODIUM ION(Non-functional Binders)

NA.4: 3 residues within 4Å: Chain A: Y.257, P.406, Q.410 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.261, A:P.406 Water bridges: A:E.203 NA.5: 5 residues within 4Å: Chain A: P.383, K.384, P.385, F.391, I.392 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.383, A:I.392 NA.10: 5 residues within 4Å: Chain B: P.273, E.274, Q.413, N.416, R.417 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.273, B:N.416, B:R.417 Water bridges: B:F.275 NA.16: 3 residues within 4Å: Chain C: Y.257, P.406, Q.410 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.257, C:R.261 Water bridges: C:E.203 NA.17: 5 residues within 4Å: Chain C: P.383, K.384, P.385, F.391, I.392 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.392, C:I.392 NA.22: 5 residues within 4Å: Chain D: P.273, E.274, Q.413, N.416, R.417 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.413, D:N.416, D:R.417 Water bridges: D:F.275 NA.28: 3 residues within 4Å: Chain E: Y.257, P.406, Q.410 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Y.257, E:R.261 Water bridges: E:E.203 NA.29: 5 residues within 4Å: Chain E: P.383, K.384, P.385, F.391, I.392 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:I.392, E:I.392 NA.34: 5 residues within 4Å: Chain F: P.273, E.274, Q.413, N.416, R.417 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:Q.413, F:N.416, F:R.417 Water bridges: F:F.275

15 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.6: 6 residues within 4Å: Chain A: H.223, F.228, Y.250, Q.353, E.372, Y.399 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.399 SCN.7: 2 residues within 4Å: Chain A: T.578, N.582 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.582 SCN.8: 5 residues within 4Å: Chain A: Y.144, R.484, K.558, D.560, S.561 No protein-ligand interaction detected (PLIP) SCN.11: 6 residues within 4Å: Chain B: H.226, F.231, Y.253, Q.356, E.375, Y.402 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.253, B:Q.356, B:Y.402 SCN.12: 6 residues within 4Å: Chain B: N.195, Y.196, N.198, A.199, P.669, Y.670 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.196 SCN.18: 6 residues within 4Å: Chain C: H.223, F.228, Y.250, Q.353, E.372, Y.399 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.399 SCN.19: 2 residues within 4Å: Chain C: T.578, N.582 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.582 SCN.20: 5 residues within 4Å: Chain C: Y.144, R.484, K.558, D.560, S.561 No protein-ligand interaction detected (PLIP) SCN.23: 6 residues within 4Å: Chain D: H.226, F.231, Y.253, Q.356, E.375, Y.402 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.253, D:Q.356, D:Y.402 SCN.24: 6 residues within 4Å: Chain D: N.195, Y.196, N.198, A.199, P.669, Y.670 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.196 SCN.30: 6 residues within 4Å: Chain E: H.223, F.228, Y.250, Q.353, E.372, Y.399 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Y.399 SCN.31: 2 residues within 4Å: Chain E: T.578, N.582 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.582 SCN.32: 5 residues within 4Å: Chain E: Y.144, R.484, K.558, D.560, S.561 No protein-ligand interaction detected (PLIP) SCN.35: 6 residues within 4Å: Chain F: H.226, F.231, Y.253, Q.356, E.375, Y.402 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:Y.253, F:Q.356, F:Y.402 SCN.36: 6 residues within 4Å: Chain F: N.195, Y.196, N.198, A.199, P.669, Y.670 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:Y.196

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pietrzyk, A.J. et al., Crystallographic identification of an unexpected protein complex in silkworm haemolymph. Acta Crystallogr.,Sect.D (2013)

Release Date

2013-12-04

Peptides

Silkworm storage protein: ACE
Arylphorin: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

Silkworm storage protein

Arylphorin