SMTL ID : 3fu8.1

Melanocarpus albomyces laccase crystal soaked (10 sec) with 2,6-dimethoxyphenol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Post Translational Modification)

NAG-NAG-MAN-MAN.1: 15 residues within 4Å: Chain A: E.42, E.55, K.56, M.58, T.87, N.88, F.141, R.178, A.179, D.181, D.182, W.384, N.550, Y.552, P.553 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.178, A:R.178, A:D.182, A:D.181, A:D.182 Water bridges: A:R.178, A:E.55, A:D.181, A:D.182 Hydrophobic interactions: A:K.56, A:A.179 NAG-NAG-MAN-MAN.6: 12 residues within 4Å: Chain B: E.55, K.56, M.58, T.87, N.88, R.178, A.179, D.181, D.182, N.550, Y.552, P.553 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.55, B:R.178, B:D.181, B:D.182, B:D.182 Water bridges: B:R.178, B:R.178, B:R.178, B:E.55, B:A.180 Hydrophobic interactions: B:A.179

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

NAG-NAG.2: 8 residues within 4Å: Chain A: N.216, T.218, I.309, H.311, A.313, G.314, G.317, G.318 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.314 NAG-NAG.4: 7 residues within 4Å: Chain A: P.355, D.356, T.358, L.359, N.376, V.406, W.417 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 6 residues within 4Å: Chain A: L.167, V.169, F.170, N.201, N.216, V.217 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 8 residues within 4Å: Chain B: N.216, T.218, I.309, H.311, A.313, G.314, G.317, G.318 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.314, B:A.315 Water bridges: B:G.318 NAG-NAG.9: 7 residues within 4Å: Chain B: P.355, D.356, T.358, L.359, N.376, V.406, W.417 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.356 Water bridges: B:D.356

2 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Post Translational Modification)

NAG-NAG-MAN.3: 9 residues within 4Å: Chain A: Y.214, W.287, N.289, T.291, H.305, A.307, E.323, T.325, P.326 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.287 Water bridges: A:E.323 NAG-NAG-MAN.8: 9 residues within 4Å: Chain B: Y.214, W.287, N.289, T.291, H.305, A.307, L.319, E.323, T.325 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.287, B:L.319 Water bridges: B:Y.214, B:Y.214

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

CU.10: 5 residues within 4Å: Chain A: H.431, C.503, I.505, H.508, L.513 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.431, A:C.503, A:H.508 CU.11: 3 residues within 4Å: Chain A: H.140, H.436, H.502 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.140, A:H.436, A:H.502, H2O.23 CU.12: 5 residues within 4Å: Chain A: H.93, H.95, W.136, H.138, H.504 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.95, A:H.138, A:H.504, H2O.23 CU.13: 5 residues within 4Å: Chain A: H.93, H.95, H.434, H.436 Ligands: CL.14 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.93, A:H.434 CU.21: 5 residues within 4Å: Chain B: H.431, C.503, I.505, H.508, L.513 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.431, B:C.503, B:H.508 CU.22: 3 residues within 4Å: Chain B: H.140, H.436, H.502 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.140, B:H.436, B:H.502, H2O.32 CU.23: 4 residues within 4Å: Chain B: H.95, W.136, H.138, H.504 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.95, B:H.138, B:H.504, H2O.32 CU.24: 5 residues within 4Å: Chain B: H.93, H.95, H.434, H.436 Ligands: CL.25 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.93, B:H.434

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

CL.14: 7 residues within 4Å: Chain A: H.93, W.94, H.95, G.96, H.434, H.436 Ligands: CU.13 Ligand excluded by PLIP CL.25: 7 residues within 4Å: Chain B: H.93, W.94, H.95, G.96, H.434, H.436 Ligands: CU.24 Ligand excluded by PLIP

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

NAG.15: 3 residues within 4Å: Chain A: N.39, I.82, N.84 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.82 Hydrogen bonds: A:N.84 Water bridges: A:N.84 NAG.16: 3 residues within 4Å: Chain A: K.386, Y.391, N.396 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.391, A:Y.391, A:N.396 NAG.26: 3 residues within 4Å: Chain B: N.39, T.41, N.84 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.39, B:N.84 Water bridges: B:N.84 NAG.27: 3 residues within 4Å: Chain B: K.386, Y.391, N.396 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.386 Water bridges: B:Y.391, B:Y.391, B:T.394, B:T.394 NAG.28: 4 residues within 4Å: Chain B: L.167, F.170, N.201, V.217 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.170 Hydrogen bonds: B:V.169, B:N.201 Water bridges: B:L.167, B:L.167

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

SO4.17: 2 residues within 4Å: Chain A: R.128, R.130 5 PLIP interactions: 5 interactions with chain A Water bridges: A:T.27, A:R.130, A:R.130 Salt bridges: A:R.128, A:R.130 SO4.18: 2 residues within 4Å: Chain A: R.520, R.527 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.527 Salt bridges: A:R.520, A:R.527 SO4.29: 2 residues within 4Å: Chain B: R.128, R.130 4 PLIP interactions: 4 interactions with chain B Water bridges: B:T.27, B:R.128 Salt bridges: B:R.128, B:R.130

2 x 3DM: 2,6-dimethoxyphenol(Non-covalent)

3DM.19: 10 residues within 4Å: Chain A: A.191, P.192, A.296, A.297, F.371, W.373, L.429, H.508 Ligands: GOL.20, GOL.31 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.191, A:L.429 Hydrogen bonds: A:H.508 3DM.30: 11 residues within 4Å: Chain B: A.191, P.192, E.235, A.296, A.297, F.371, F.427, L.429, H.508 Ligands: GOL.20, GOL.31 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:A.191, B:F.427, B:L.429, B:L.429 Hydrogen bonds: B:H.508

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.20: 6 residues within 4Å: Chain A: F.427 Chain B: F.371, F.427 Ligands: 3DM.19, 3DM.30, GOL.31 No protein-ligand interaction detected (PLIP) GOL.31: 5 residues within 4Å: Chain A: F.427 Chain B: F.427 Ligands: 3DM.19, GOL.20, 3DM.30 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kallio, J.P. et al., Structure-Function Studies of a Melanocarpus albomyces Laccase Suggest a Pathway for Oxidation of Phenolic Compounds. J.Mol.Biol. (2009)

Release Date

2009-09-22

Peptides

Laccase-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Laccase-1

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