SMTL ID : 3fu9.1

Melanocarpus albomyces laccase crystal soaked (20 min) with 2,6-dimethoxyphenol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

4 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: 13 residues within 4Å: Chain A: E.42, E.55, K.56, M.58, T.87, N.88, A.179, D.181, D.182, W.547, N.550, Y.552, P.553 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.179 Hydrogen bonds: A:D.181, A:D.182 NAG-NAG.2: 8 residues within 4Å: Chain A: Y.214, W.287, N.289, H.305, A.307, E.323, T.325, P.326 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.287 NAG-NAG.3: 14 residues within 4Å: Chain B: E.42, E.55, K.56, M.58, T.87, N.88, F.141, A.179, D.181, D.182, W.384, N.550, Y.552, P.553 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.179 Hydrogen bonds: B:D.181, B:D.182 Water bridges: B:D.181 NAG-NAG.4: 9 residues within 4Å: Chain B: V.243, W.287, N.289, H.305, A.307, E.323, G.324, T.325, P.326 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.323

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

CU.5: 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.6: 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.1 CU.7: 6 residues within 4Å: Chain A: H.93, H.95, W.136, H.138, H.504 Ligands: CU.8 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.95, A:H.138, A:H.504, H2O.1 CU.8: 6 residues within 4Å: Chain A: H.93, H.95, H.434, H.436 Ligands: CU.7, CL.9 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.93, A:H.434 CU.15: 4 residues within 4Å: Chain B: H.431, C.503, H.508, L.513 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.431, B:C.503, B:H.508 CU.16: 5 residues within 4Å: Chain B: H.140, H.434, H.436, L.500, 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.15 CU.17: 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.15 CU.18: 5 residues within 4Å: Chain B: H.93, H.95, H.434, H.436 Ligands: CL.19 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.93, B:H.434, B:H.436

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

CL.9: 7 residues within 4Å: Chain A: H.93, G.96, H.434, L.435, H.436, G.437 Ligands: CU.8 Ligand excluded by PLIP CL.19: 8 residues within 4Å: Chain B: H.93, W.94, H.95, G.96, H.434, L.435, H.436 Ligands: CU.18 Ligand excluded by PLIP

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

NAG.10: 2 residues within 4Å: Chain A: N.39, N.84 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.84 Water bridges: A:N.39, A:N.84 NAG.11: 4 residues within 4Å: Chain A: N.216, T.218, I.309, H.311 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.216, A:I.309 Water bridges: A:T.218, A:H.311 NAG.12: 6 residues within 4Å: Chain A: P.355, D.356, T.358, L.359, N.376, V.406 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.359 Hydrogen bonds: A:P.355, A:P.355, A:N.376 NAG.20: 4 residues within 4Å: Chain B: N.39, T.41, I.82, N.84 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.82 Hydrogen bonds: B:N.39 NAG.21: 6 residues within 4Å: Chain B: N.216, T.218, I.309, H.311, G.317, G.318 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.309 Hydrogen bonds: B:N.216 Water bridges: B:P.316, B:G.318 NAG.22: 6 residues within 4Å: Chain B: P.355, D.356, T.358, L.359, N.376, W.417 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.359, B:W.417 Hydrogen bonds: B:P.355, B:P.355, B:N.376 NAG.23: 6 residues within 4Å: Chain B: L.167, V.169, F.170, N.201, N.216, V.217 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.170, B:V.217 Hydrogen bonds: B:V.169, B:N.201 Water bridges: B:N.216

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

SO4.13: 2 residues within 4Å: Chain A: R.128, R.130 4 PLIP interactions: 4 interactions with chain A Water bridges: A:T.27, A:R.128 Salt bridges: A:R.128, A:R.130 SO4.24: 3 residues within 4Å: Chain B: T.27, R.128, R.130 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.27, B:T.27 Salt bridges: B:R.128, B:R.130

2 x KIB: 2,6-dimethoxybenzene-1,4-diol(Non-covalent)

KIB.14: 8 residues within 4Å: Chain A: A.191, P.192, A.296, A.297, F.371, F.427, L.429, H.508 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.429 KIB.25: 6 residues within 4Å: Chain B: A.191, P.192, A.296, A.297, L.429, H.508 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.191, B:L.429 Hydrogen bonds: B:H.508

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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