SMTL ID : 3x1b.1

Crystal structure of laccase from Lentinus sp. at 1.8 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA- MAN- MAN- MAN: 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.1: 13 residues within 4Å: Chain A: Y.41, R.43, D.44, N.75, T.77, M.78, H.174, T.175, A.176, L.179, T.201 Chain B: A.202, N.293 7 PLIP interactions: 1 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:N.293, A:A.176 Hydrophobic interactions: A:R.43, A:A.176 Water bridges: A:Y.41, A:Y.41, A:Y.41 NAG-NAG-BMA-MAN-MAN-MAN.2: 10 residues within 4Å: Chain A: G.342, V.344, D.345, K.346, A.347, L.348, N.349, S.405, P.407, N.458 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.342, A:K.346, A:A.347 Hydrophobic interactions: A:A.347 Water bridges: A:N.349, A:N.349

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(Post Translational Modification)

NAG-NAG-BMA-MAN-MAN-MAN.3: 11 residues within 4Å: Chain B: Y.41, R.43, D.44, N.75, T.77, M.78, H.174, T.175, A.176, L.179, T.201 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:R.43, B:A.176 Hydrogen bonds: B:A.176 Water bridges: B:Y.41, B:D.44

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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(Non-covalent)

NAG-NAG-BMA-MAN-MAN-MAN-MAN.4: 10 residues within 4Å: Chain B: G.342, V.344, D.345, K.346, A.347, L.348, N.349, S.405, P.407, N.458 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.347

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

NAG.5: 3 residues within 4Å: Chain A: G.236, N.238, T.320 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.238, A:T.320 NAG.10: 3 residues within 4Å: Chain B: G.236, N.238, Q.273 3 PLIP interactions: 3 interactions with chain B Water bridges: B:N.238, B:T.320, B:T.320

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

CU.6: 5 residues within 4Å: Chain A: H.85, H.87, H.420, H.422 Ligands: CU.7 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.85, A:H.420, H2O.2 CU.7: 6 residues within 4Å: Chain A: H.85, H.87, W.128, H.130, H.476 Ligands: CU.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.87, A:H.130, A:H.476, H2O.1 CU.8: 3 residues within 4Å: Chain A: H.132, H.422, H.474 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.132, A:H.422, A:H.474, H2O.1 CU.9: 5 residues within 4Å: Chain A: H.417, C.475, I.477, H.480, F.485 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.417, A:C.475, A:H.480 CU.11: 5 residues within 4Å: Chain B: H.85, H.87, H.420, H.422 Ligands: CU.12 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.85, B:H.420, H2O.24 CU.12: 6 residues within 4Å: Chain B: H.85, H.87, W.128, H.130, H.476 Ligands: CU.11 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.87, B:H.130, B:H.476, H2O.25 CU.13: 3 residues within 4Å: Chain B: H.132, H.422, H.474 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.132, B:H.422, B:H.474, H2O.25 CU.14: 5 residues within 4Å: Chain B: H.417, C.475, I.477, H.480, F.485 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.417, B:C.475, B:H.480

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, W.C. et al., Crystal structure of laccase from Lentinus sp. at 1.8 A resolution. To be Published

Release Date

2014-12-10

Peptides

laccase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

laccase