SMTL ID : 8po9.1

Polyethylene oxidation hexamerin PEase Cibeles (XP_026756460) from Galleria mellonella

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

1 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.1: 16 residues within 4Å: Chain A: Y.209, N.211, Y.689, Y.690, N.691, S.692, W.694, S.695 Chain D: A.88, G.89, F.90, P.92 Chain E: S.544, L.545, E.546, P.665 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A Water bridges: D:K.93 Hydrophobic interactions: A:Y.690 Hydrogen bonds: A:S.692

7 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

NAG-NAG-BMA-MAN-MAN.2: 14 residues within 4Å: Chain A: E.46, N.47, N.481, T.483, D.494, T.495, V.496, S.497, S.499, I.501, S.585, L.586, F.587, Y.590 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.494, A:E.46, A:S.497 NAG-NAG-BMA-MAN-MAN.5: 10 residues within 4Å: Chain C: Y.209, N.211, Y.689, Y.690, N.691, S.692, W.694, S.695 Chain F: F.90, P.92 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Y.690 Hydrogen bonds: C:S.692 Water bridges: C:S.695 NAG-NAG-BMA-MAN-MAN.7: 10 residues within 4Å: Chain A: G.89, F.90, P.92 Chain D: Y.209, N.211, Y.689, Y.690, N.691, S.692, W.694 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:A.88, D:S.692 Hydrophobic interactions: D:Y.690 Water bridges: D:Y.196 NAG-NAG-BMA-MAN-MAN.8: 14 residues within 4Å: Chain D: T.39, E.46, N.47, N.481, T.483, D.494, T.495, V.496, S.497, S.499, I.501, L.586, F.587, Y.590 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.46, D:S.497 NAG-NAG-BMA-MAN-MAN.9: 6 residues within 4Å: Chain B: G.89, F.90, I.91, P.92 Chain E: Y.209, N.211 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.10: 13 residues within 4Å: Chain E: E.46, N.47, N.481, T.483, D.494, T.495, V.496, S.497, S.499, I.501, L.586, F.587, Y.590 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.494, E:E.46, E:S.497 NAG-NAG-BMA-MAN-MAN.12: 12 residues within 4Å: Chain F: E.46, N.47, N.481, T.483, D.494, V.496, S.497, S.499, I.501, L.586, F.587, Y.590 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:D.494, F:E.46, F:S.497

2 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.3: 3 residues within 4Å: Chain B: Y.209, N.211, Y.689 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 11 residues within 4Å: Chain C: E.46, N.47, N.481, T.483, T.495, V.496, S.497, S.499, I.501, L.586, F.587 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.46, C:E.46, C:S.497

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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-MAN-MAN.4: 13 residues within 4Å: Chain B: E.46, N.47, N.481, T.483, D.494, T.495, V.496, S.497, S.499, I.501, L.586, F.587, Y.590 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.46, B:S.497

1 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.11: 14 residues within 4Å: Chain B: P.542 Chain C: Y.86, G.89, F.90, P.92, W.134 Chain F: Y.209, N.211, Y.689, Y.690, N.691, S.692, W.694 Ligands: GLY.44 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain F Hydrophobic interactions: B:P.542 Hydrogen bonds: F:S.692, F:S.695

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

CU.13: 4 residues within 4Å: Chain A: E.219, D.220, Q.299, D.318 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.219, A:Q.299, A:D.318, H2O.4, H2O.6 CU.23: 4 residues within 4Å: Chain B: E.219, D.220, Q.299, D.318 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.219, B:Q.299, B:D.318, H2O.14, H2O.19 CU.34: 4 residues within 4Å: Chain C: E.219, D.220, Q.299, D.318 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.219, C:Q.299, C:D.318, H2O.27, H2O.28 CU.45: 4 residues within 4Å: Chain D: E.219, D.220, Q.299, D.318 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.219, D:Q.299, D:D.318, H2O.35, H2O.38 CU.58: 4 residues within 4Å: Chain E: E.219, D.220, Q.299, D.318 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.219, E:Q.299, E:D.318, H2O.45, H2O.47 CU.68: 4 residues within 4Å: Chain F: E.219, D.220, Q.299, D.318 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.219, F:Q.299, F:D.318, H2O.52, H2O.56

5 x MG: MAGNESIUM ION(Non-covalent)

MG.14: 4 residues within 4Å: Chain A: S.406, Y.409, M.412, N.413 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:S.406, A:Y.409, A:M.412 MG.24: 5 residues within 4Å: Chain B: S.406, Y.409, E.410, M.412, N.413 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.406, B:Y.409, B:M.412, H2O.22 MG.35: 5 residues within 4Å: Chain C: S.406, Y.409, E.410, M.412, N.413 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:S.406, C:Y.409, C:M.412, H2O.30 MG.59: 4 residues within 4Å: Chain E: S.406, Y.409, M.412, N.413 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:S.406, E:Y.409, E:M.412, H2O.49 MG.69: 5 residues within 4Å: Chain F: S.406, Y.409, E.410, M.412, N.413 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:S.406, F:Y.409, F:M.412, H2O.60

22 x CL: CHLORIDE ION(Non-functional Binders)

CL.15: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain B: Y.674, F.675 Ligand excluded by PLIP CL.26: 1 residues within 4Å: Chain B: S.564 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain A: K.347 Chain B: K.347 Chain C: K.347 Ligand excluded by PLIP CL.28: 1 residues within 4Å: Chain B: V.66 Ligand excluded by PLIP CL.36: 1 residues within 4Å: Chain C: W.388 Ligand excluded by PLIP CL.37: 1 residues within 4Å: Chain C: F.130 Ligand excluded by PLIP CL.38: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.39: 1 residues within 4Å: Ligands: CL.40 Ligand excluded by PLIP CL.40: 4 residues within 4Å: Chain C: Q.185, L.188, I.189 Ligands: CL.39 Ligand excluded by PLIP CL.46: 3 residues within 4Å: Chain D: G.187, L.188, Y.206 Ligand excluded by PLIP CL.47: 2 residues within 4Å: Chain D: I.99, W.388 Ligand excluded by PLIP CL.48: 3 residues within 4Å: Chain D: Q.185, I.189, I.190 Ligand excluded by PLIP CL.49: 2 residues within 4Å: Chain D: V.66, F.130 Ligand excluded by PLIP CL.50: 1 residues within 4Å: Chain D: W.388 Ligand excluded by PLIP CL.51: 1 residues within 4Å: Chain D: Y.309 Ligand excluded by PLIP CL.52: 2 residues within 4Å: Chain D: K.580, S.583 Ligand excluded by PLIP CL.60: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.61: 1 residues within 4Å: Chain E: P.195 Ligand excluded by PLIP CL.62: 1 residues within 4Å: Chain E: V.66 Ligand excluded by PLIP CL.70: 3 residues within 4Å: Chain F: Q.185, I.189, I.190 Ligand excluded by PLIP CL.71: 1 residues within 4Å: Chain F: E.56 Ligand excluded by PLIP

3 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.16: 10 residues within 4Å: Chain A: K.178, R.181, I.182, Q.185, L.188, I.189, I.190, Y.197, I.199 Chain D: N.94 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.185, A:I.189, A:I.190 Water bridges: A:R.181 Salt bridges: A:R.181 MES.29: 8 residues within 4Å: Chain B: K.178, R.181, I.182, Q.185, L.188, I.189, I.190, I.199 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.185, B:I.189, B:I.190, B:I.190 Water bridges: B:R.181, B:R.181 Salt bridges: B:R.181 MES.63: 9 residues within 4Å: Chain B: N.94 Chain E: K.178, R.181, Q.185, L.188, I.189, I.190, Y.197, I.199 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:Q.185, E:I.189, E:I.190 Water bridges: E:R.181, E:R.181 Salt bridges: E:R.181

11 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.17: 9 residues within 4Å: Chain A: L.274, A.275, Y.278, R.291, A.435, L.438, D.439, I.550, N.551 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.278, A:A.435, A:L.438 Hydrogen bonds: A:R.291, A:N.551 Water bridges: A:R.291, A:N.442 MPD.18: 6 residues within 4Å: Chain A: R.261, E.264, S.362, K.363, I.365, N.651 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.365 Hydrogen bonds: A:N.651 MPD.19: 6 residues within 4Å: Chain A: I.265, Y.268, F.578, I.607, Y.647, F.654 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.268, A:I.607, A:Y.647, A:F.654 MPD.20: 8 residues within 4Å: Chain A: Q.343, Q.346, K.347 Chain B: T.340, L.344, K.347, A.352, Y.353 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:T.340, B:A.352, B:Y.353, A:Q.346, A:K.347 MPD.30: 6 residues within 4Å: Chain B: R.261, E.264, S.362, K.363, I.365, N.651 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:K.363, B:I.365 Hydrogen bonds: B:S.362, B:N.651 Water bridges: B:R.660 MPD.31: 10 residues within 4Å: Chain B: L.274, A.275, Y.278, I.289, R.291, A.435, L.438, D.439, I.550, N.551 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.278, B:I.289, B:A.435, B:L.438 Hydrogen bonds: B:R.291, B:N.551 Water bridges: B:R.291, B:N.442 MPD.41: 10 residues within 4Å: Chain C: L.274, A.275, Y.278, R.291, A.435, L.438, D.439, N.442, I.550, N.551 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:L.274, C:L.274, C:Y.278, C:L.438 Hydrogen bonds: C:R.291, C:N.442, C:N.551 Water bridges: C:R.291, C:D.439 MPD.54: 9 residues within 4Å: Chain D: L.274, Y.278, I.289, R.291, A.435, L.438, D.439, I.550, N.551 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:Y.278, D:I.289, D:L.438 Hydrogen bonds: D:R.291, D:N.551 Water bridges: D:R.291, D:R.291 MPD.55: 6 residues within 4Å: Chain D: R.261, E.264, S.362, K.363, N.651, P.653 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:K.363, D:P.653, D:P.653 Hydrogen bonds: D:R.261 MPD.64: 10 residues within 4Å: Chain E: L.274, A.275, Y.278, I.289, R.291, A.435, L.438, D.439, I.550, N.551 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:Y.278, E:I.289, E:A.435, E:L.438 Hydrogen bonds: E:R.291, E:N.551 Water bridges: E:N.442 MPD.73: 10 residues within 4Å: Chain F: L.274, A.275, Y.278, I.289, R.291, A.435, L.438, D.439, I.550, N.551 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:Y.278, F:I.289, F:L.438 Hydrogen bonds: F:R.291, F:N.551 Water bridges: F:R.291, F:N.442

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.21: 7 residues within 4Å: Chain A: V.468, D.469, K.470, L.471, V.678, Y.679, Y.681 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.468, A:L.471, A:L.471, A:Y.679, A:Y.679 Water bridges: A:V.468 GOL.22: 9 residues within 4Å: Chain A: F.97, S.98, I.99, Y.142, Y.239, D.419, F.420, Y.421, Q.422 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.99, A:Y.421, A:Q.422 Water bridges: A:W.166 GOL.32: 9 residues within 4Å: Chain B: F.97, S.98, I.99, Y.142, Y.239, D.419, F.420, Y.421, Q.422 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.98, B:I.99, B:W.166, B:Y.239, B:Y.421, B:Q.422, B:Q.422 GOL.33: 8 residues within 4Å: Chain B: V.468, D.469, K.470, L.471, K.676, V.678, Y.679, Y.681 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.471, B:Y.679, B:Y.679 Water bridges: B:V.468, B:K.676 GOL.42: 2 residues within 4Å: Chain A: Y.353 Chain C: K.347 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.353 Water bridges: A:T.340, A:Y.353 GOL.65: 10 residues within 4Å: Chain E: F.97, S.98, I.99, Y.142, W.166, Y.239, D.419, F.420, Y.421, Q.422 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:S.98, E:I.99, E:W.166, E:Y.421, E:Q.422, E:Q.422

7 x GLY: GLYCINE(Non-covalent)

GLY.43: 9 residues within 4Å: Chain C: F.97, S.98, I.99, Y.142, Y.239, D.419, F.420, Y.421, Q.422 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.98, C:I.99, C:W.166, C:Y.239, C:Y.421, C:Q.422 GLY.44: 3 residues within 4Å: Chain C: A.88, G.89 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.11 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.88 GLY.56: 1 residues within 4Å: Chain D: K.347 No protein-ligand interaction detected (PLIP) GLY.57: 9 residues within 4Å: Chain D: F.97, S.98, I.99, Y.142, Y.239, D.419, F.420, Y.421, Q.422 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.98, D:I.99, D:Y.239, D:Y.421, D:Q.422 GLY.66: 3 residues within 4Å: Chain D: T.340, K.347 Chain E: K.347 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:Y.353 Water bridges: D:Y.353, D:Y.353 Salt bridges: E:K.347 GLY.67: 7 residues within 4Å: Chain E: V.468, D.469, K.470, L.471, V.678, Y.679, Y.681 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:V.468, E:D.469, E:L.471, E:Y.679 Water bridges: E:K.676 GLY.74: 9 residues within 4Å: Chain F: F.97, S.98, I.99, Y.142, Y.239, D.419, F.420, Y.421, Q.422 7 PLIP interactions: 1 Ligand-Ligand interactions, 6 interactions with chain F Hydrogen bonds: G.74, F:I.99, F:Y.239, F:Y.239, F:Y.421, F:Q.422, F:Q.422

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

SO4.53: 3 residues within 4Å: Chain D: K.347 Chain E: K.347 Chain F: K.347 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E, 1 interactions with chain F Salt bridges: D:K.347, E:K.347, F:K.347 SO4.72: 3 residues within 4Å: Chain E: T.340 Chain F: Q.343, K.347 2 PLIP interactions: 2 interactions with chain F Water bridges: F:K.347 Salt bridges: F:K.347

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: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Arylphorin

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