SMTL ID : 8can.1

Cryo-EM structure of the Cora homohexamer from Galleria mellonella saliva

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

6 x TRP: TRYPTOPHAN(Non-covalent)

TRP.1: 15 residues within 4Å: Chain A: Y.244, G.275, Q.278, L.279, R.282, V.559, E.560, I.561, N.583, N.584, V.585, F.618, L.623, R.664, W.665 11 PLIP interactions: 8 interactions with chain A, 3 Ligand-Ligand interactions Hydrophobic interactions: A:Q.278, A:F.618 Hydrogen bonds: A:N.584, A:W.665, A:W.665, W.1, W.1 Water bridges: A:E.560, W.1 pi-Stacking: A:F.618, A:F.618 TRP.6: 15 residues within 4Å: Chain B: Y.244, G.275, Q.278, L.279, R.282, V.559, E.560, I.561, N.583, N.584, V.585, F.618, L.623, R.664, W.665 14 PLIP interactions: 10 interactions with chain B, 4 Ligand-Ligand interactions Hydrophobic interactions: B:Q.278, B:F.618 Hydrogen bonds: B:N.584, B:W.665, B:W.665, W.6, W.6 Water bridges: B:E.560, B:E.560, B:I.561, W.6, W.6 pi-Stacking: B:F.618, B:F.618 TRP.12: 15 residues within 4Å: Chain C: Y.244, G.275, Q.278, L.279, R.282, V.559, E.560, I.561, N.583, N.584, V.585, F.618, L.623, R.664, W.665 11 PLIP interactions: 8 interactions with chain C, 3 Ligand-Ligand interactions Hydrophobic interactions: C:Q.278, C:F.618 Hydrogen bonds: C:N.584, C:W.665, C:W.665, W.12, W.12 Water bridges: C:E.560, W.12 pi-Stacking: C:F.618, C:F.618 TRP.19: 15 residues within 4Å: Chain D: Y.244, G.275, Q.278, L.279, R.282, V.559, E.560, I.561, N.583, N.584, V.585, F.618, L.623, R.664, W.665 9 PLIP interactions: 8 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:Q.278, D:F.618 Hydrogen bonds: D:N.584, D:W.665, D:W.665 Water bridges: D:E.560, W.19 pi-Stacking: D:F.618, D:F.618 TRP.24: 15 residues within 4Å: Chain E: Y.244, G.275, Q.278, L.279, R.282, V.559, E.560, I.561, N.583, N.584, V.585, F.618, L.623, R.664, W.665 12 PLIP interactions: 10 interactions with chain E, 2 Ligand-Ligand interactions Hydrophobic interactions: E:Q.278, E:F.618 Hydrogen bonds: E:N.584, E:W.665, E:W.665 Water bridges: E:E.560, E:E.560, E:I.561, W.24, W.24 pi-Stacking: E:F.618, E:F.618 TRP.30: 15 residues within 4Å: Chain F: Y.244, G.275, Q.278, L.279, R.282, V.559, E.560, I.561, N.583, N.584, V.585, F.618, L.623, R.664, W.665 10 PLIP interactions: 9 interactions with chain F, 1 Ligand-Ligand interactions Hydrophobic interactions: F:Q.278, F:F.618 Hydrogen bonds: F:N.584, F:W.665, F:W.665 Water bridges: F:Y.244, F:E.560, W.30 pi-Stacking: F:F.618, F:F.618

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

CU.2: 4 residues within 4Å: Chain A: H.360, H.390, K.393 Chain C: M.451 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.360, A:H.390 CU.3: 2 residues within 4Å: Chain A: H.54, H.500 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.54, A:H.500, H2O.3 CU.4: 5 residues within 4Å: Chain A: H.515, S.579, V.585, H.620, L.623 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.515, A:H.620 CU.5: 3 residues within 4Å: Chain A: R.231, H.290 Chain D: H.291 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: A:H.290, D:H.291, H2O.18 CU.7: 4 residues within 4Å: Chain A: M.451 Chain B: H.360, H.390, K.393 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.360, B:H.390 CU.8: 2 residues within 4Å: Chain B: H.54, H.500 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.54, B:H.500, H2O.28 CU.9: 5 residues within 4Å: Chain B: H.515, S.579, V.585, H.620, L.623 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.515, B:H.620 CU.10: 3 residues within 4Å: Chain B: R.231, H.290 Chain F: H.291 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain F Metal complexes: B:H.290, F:H.291 CU.13: 4 residues within 4Å: Chain B: M.451 Chain C: H.360, H.390, K.393 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.360, C:H.390 CU.14: 2 residues within 4Å: Chain C: H.54, H.500 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.54, C:H.500, H2O.49 CU.15: 5 residues within 4Å: Chain C: H.515, S.579, V.585, H.620, L.623 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.515, C:H.620 CU.16: 3 residues within 4Å: Chain C: R.231, H.290 Chain E: H.291 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: E:H.291, C:H.290, H2O.99 CU.18: 3 residues within 4Å: Chain A: H.291 Chain D: R.231, H.290 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: A:H.291, D:H.290, H2O.79 CU.20: 4 residues within 4Å: Chain D: H.360, H.390, K.393 Chain F: M.451 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:H.360, D:H.390 CU.21: 2 residues within 4Å: Chain D: H.54, H.500 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.54, D:H.500, H2O.64 CU.22: 5 residues within 4Å: Chain D: H.515, S.579, V.585, H.620, L.623 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:H.515, D:H.620 CU.23: 3 residues within 4Å: Chain C: H.291 Chain E: R.231, H.290 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain C Metal complexes: E:H.290, C:H.291 CU.25: 4 residues within 4Å: Chain D: M.451 Chain E: H.360, H.390, K.393 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:H.360, E:H.390 CU.26: 2 residues within 4Å: Chain E: H.54, H.500 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.54, E:H.500, H2O.90 CU.27: 5 residues within 4Å: Chain E: H.515, S.579, V.585, H.620, L.623 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:H.515, E:H.620 CU.29: 3 residues within 4Å: Chain B: H.291 Chain F: R.231, H.290 3 PLIP interactions: 1 interactions with chain F, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: F:H.290, B:H.291, H2O.38 CU.31: 4 residues within 4Å: Chain E: M.451 Chain F: H.360, H.390, K.393 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:H.360, F:H.390 CU.32: 2 residues within 4Å: Chain F: H.54, H.500 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.54, F:H.500, H2O.110 CU.33: 5 residues within 4Å: Chain F: H.515, S.579, V.585, H.620, L.623 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:H.515, F:H.620

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

NA.11: 4 residues within 4Å: Chain B: Y.324, M.327 Chain D: Y.324, M.327 No protein-ligand interaction detected (PLIP) NA.17: 4 residues within 4Å: Chain C: Y.324, M.327 Chain F: Y.324, M.327 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain F Water bridges: C:N.325, F:N.325 NA.28: 4 residues within 4Å: Chain A: Y.324, M.327 Chain E: Y.324, M.327 No protein-ligand interaction detected (PLIP)

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

basic juvenile hormone-suppressible protein 1: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

basic juvenile hormone-suppressible protein 1