SMTL ID : 6kli.1

Crystal Structure of the Zea Mays laccase 3 complexed with sinapyl

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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

NAG-NAG.1: 6 residues within 4Å: Chain A: N.55, Y.76, P.81, Q.83, K.549, C.550 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.83, A:C.550 NAG-NAG.2: 8 residues within 4Å: Chain A: N.373, P.404, F.405, F.407, L.418, F.420, T.421, K.422 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.420

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

CU.3: 5 residues within 4Å: Chain A: H.451, C.514, F.516, H.519, M.524 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.451, A:C.514, A:H.519 CU.4: 7 residues within 4Å: Chain A: H.59, H.61, H.454, H.456 Ligands: CU.5, CU.6, OXY.14 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.59, A:H.454, H2O.11 CU.5: 6 residues within 4Å: Chain A: H.106, H.454, H.456, H.513 Ligands: CU.4, OXY.14 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.106, A:H.456, A:H.513 CU.6: 6 residues within 4Å: Chain A: H.61, W.102, H.104, H.515 Ligands: CU.4, OXY.14 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.61, A:H.104, A:H.515

5 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.7: 3 residues within 4Å: Chain A: Y.49, N.87, N.546 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.49 Water bridges: A:N.87 NAG.8: 4 residues within 4Å: Chain A: F.178, N.282, S.303, P.304 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.282 Water bridges: A:R.268 NAG.9: 4 residues within 4Å: Chain A: A.147, Q.151, E.155, N.164 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.155, A:N.164 Water bridges: A:E.155 NAG.10: 1 residues within 4Å: Chain A: N.356 4 PLIP interactions: 4 interactions with chain A Water bridges: A:N.356, A:N.356, A:N.356, A:N.356 NAG.11: 3 residues within 4Å: Chain A: N.408, A.411, P.412 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.408 Water bridges: A:N.469

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 9 residues within 4Å: Chain A: H.104, A.105, H.106, E.108, R.111, H.513, H.515, D.517 Ligands: OXY.14 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.108 Water bridges: A:H.106, A:H.106, A:R.111

1 x 55B: 4-[(1E)-3-hydroxyprop-1-en-1-yl]-2,6-dimethoxyphenol(Non-covalent)

55B.13: 14 residues within 4Å: Chain A: D.162, N.273, V.276, V.348, A.360, G.361, P.362, L.367, L.446, G.447, E.449, R.518, H.519, W.522 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.276, A:V.348, A:L.367 Hydrogen bonds: A:A.360, A:E.449, A:R.518

1 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.14: 12 residues within 4Å: Chain A: H.59, H.61, H.104, H.106, H.454, H.456, H.513, H.515 Ligands: CU.4, CU.5, CU.6, GOL.12 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xie, T. et al., Structural basis for monolignol oxidation by a maize laccase. Nat.Plants (2020)

Release Date

2020-01-01

Peptides

Laccase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Laccase

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