SMTL ID : 8ca9.1

Cryo-EM structure of the Cibeles-Demetra 3:3 heterocomplex from Galleria mellonella saliva

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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

NAG-NAG-BMA-MAN-MAN-MAN-MAN.1: 26 residues within 4Å: Chain A: K.178, Y.196, G.198, Y.209, A.210, N.211, Y.689, Y.690, N.691, S.692, Y.693, W.694, S.695 Chain D: T.88, G.89, F.90, T.91, A.92, W.134, N.409 Chain E: Y.539, P.540, D.542, E.662, S.663, Y.664 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain A Hydrogen bonds: E:S.663, E:S.663 Hydrophobic interactions: A:Y.690 Water bridges: A:S.692, A:Y.693 NAG-NAG-BMA-MAN-MAN-MAN-MAN.3: 26 residues within 4Å: Chain B: K.178, Y.196, G.198, Y.209, A.210, N.211, Y.689, Y.690, N.691, S.692, Y.693, W.694, S.695 Chain E: T.88, G.89, F.90, T.91, A.92, W.134, N.409 Chain F: Y.539, P.540, D.542, E.662, S.663, Y.664 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain B Hydrogen bonds: F:S.663, F:S.663 Hydrophobic interactions: B:Y.690 Water bridges: B:Y.693 NAG-NAG-BMA-MAN-MAN-MAN-MAN.5: 26 residues within 4Å: Chain C: K.178, Y.196, G.198, Y.209, A.210, N.211, Y.689, Y.690, N.691, S.692, Y.693, W.694, S.695 Chain D: Y.539, P.540, D.542, E.662, S.663, Y.664 Chain F: T.88, G.89, F.90, T.91, A.92, W.134, N.409 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Water bridges: C:S.692, C:S.692, C:Y.693 Hydrogen bonds: D:S.663, D:S.663 Hydrophobic interactions: C:Y.690

3 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-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.2: 22 residues within 4Å: Chain A: T.39, S.43, E.46, N.47, D.55, E.56, N.481, T.483, L.488, L.493, D.494, V.496, S.497, P.498, S.499, I.501, S.585, L.586, F.587, Y.590, L.593, S.594 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.46, A:S.497, A:S.497 NAG-NAG-BMA-MAN-MAN-MAN.4: 22 residues within 4Å: Chain B: T.39, S.43, E.46, N.47, D.55, E.56, N.481, T.483, L.488, L.493, D.494, V.496, S.497, P.498, S.499, I.501, S.585, L.586, F.587, Y.590, L.593, S.594 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.46, B:S.497, B:S.497 NAG-NAG-BMA-MAN-MAN-MAN.6: 22 residues within 4Å: Chain C: T.39, S.43, E.46, N.47, D.55, E.56, N.481, T.483, L.488, L.493, D.494, V.496, S.497, P.498, S.499, I.501, S.585, L.586, F.587, Y.590, L.593, S.594 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.46, C:S.497, C:S.497

3 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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

NAG-NAG-BMA-MAN-MAN-MAN.7: 20 residues within 4Å: Chain A: Y.86, G.89, F.90, I.91, P.92, W.134, N.411 Chain C: L.541, P.542 Chain D: K.178, G.198, Y.209, A.210, N.211, Y.687, Y.688, T.689, S.690, W.692, S.693 1 PLIP interactions: 1 interactions with chain D Water bridges: D:W.692 NAG-NAG-BMA-MAN-MAN-MAN.9: 19 residues within 4Å: Chain A: P.542 Chain B: Y.86, G.89, F.90, I.91, P.92, W.134, N.411 Chain E: K.178, G.198, Y.209, A.210, N.211, Y.687, Y.688, T.689, S.690, W.692, S.693 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.11: 20 residues within 4Å: Chain B: L.541, P.542 Chain C: Y.86, G.89, F.90, I.91, P.92, W.134, N.411 Chain F: K.178, G.198, Y.209, A.210, N.211, Y.687, Y.688, T.689, S.690, W.692, S.693 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA.8: 15 residues within 4Å: Chain D: E.46, N.47, N.479, T.481, L.486, L.491, T.493, G.494, S.495, S.497, I.499, S.583, V.584, S.585, Y.588 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.493, D:E.46, D:S.495, D:S.495 Hydrophobic interactions: D:L.486 Water bridges: D:S.585 NAG-NAG-BMA.10: 15 residues within 4Å: Chain E: E.46, N.47, N.479, T.481, L.486, L.491, T.493, G.494, S.495, S.497, I.499, S.583, V.584, S.585, Y.588 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:T.493, E:E.46, E:S.495, E:S.495 Hydrophobic interactions: E:L.486 Water bridges: E:S.585 NAG-NAG-BMA.12: 15 residues within 4Å: Chain F: E.46, N.47, N.479, T.481, L.486, L.491, T.493, G.494, S.495, S.497, I.499, S.583, V.584, S.585, Y.588 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:T.493, F:E.46, F:S.495, F:S.495 Hydrophobic interactions: F:L.486

3 x CU: COPPER (II) ION(Non-covalent)

CU.13: 4 residues within 4Å: Chain A: E.219, Q.299, T.300, D.318 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.219, A:Q.299, H2O.3, H2O.5, H2O.8 CU.14: 4 residues within 4Å: Chain B: E.219, Q.299, T.300, D.318 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.219, B:Q.299, H2O.17, H2O.20, H2O.23 CU.15: 4 residues within 4Å: Chain C: E.219, Q.299, T.300, D.318 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.219, C:Q.299, H2O.31, H2O.33, H2O.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Spinola-Amilibia, M. et al., Plastic degradation by insect hexamerins: Near-atomic resolution structures of the polyethylene-degrading proteins from the wax worm saliva. Sci Adv (2023)

Release Date

2023-10-04

Peptides

Arylphorin: ABC
Demetra: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Arylphorin

Demetra

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