SMTL ID : 2ih8.2 (1 other biounit)

A low-dose crystal structure of a recombinant Melanocarpus albomyces laccase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN: 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(Post Translational Modification)

NAG-NAG-BMA-MAN.1: 14 residues within 4Å: Chain A: E.42, E.55, K.56, M.58, T.87, N.88, R.178, A.179, D.181, D.182, W.384, N.550, Y.552, P.553 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.178, A:R.178, A:D.182, A:D.182, A:D.182 Hydrophobic interactions: A:A.179 Water bridges: A:E.55, A:D.181

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.2: 8 residues within 4Å: Chain A: N.216, T.218, I.309, H.311, A.313, G.314, G.317, G.318 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.314 Water bridges: A:G.318 NAG-NAG.4: 7 residues within 4Å: Chain A: P.355, D.356, T.358, L.359, N.376, V.406, W.417 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.356 Water bridges: A:D.356

1 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(Post Translational Modification)

NAG-NAG-BMA.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 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.287 Water bridges: A:Y.214, A:Y.214, A:E.323

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

NAG.5: 3 residues within 4Å: Chain A: N.39, T.41, N.84 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.39, A:N.84 Water bridges: A:N.84 NAG.6: 3 residues within 4Å: Chain A: K.386, Y.391, N.396 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.386 Water bridges: A:Y.391, A:N.396 NAG.7: 6 residues within 4Å: Chain A: L.167, V.169, F.170, N.201, V.217, L.227 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.167, A:F.170, A:V.217, A:L.227 Hydrogen bonds: A:V.169, A:N.201 Water bridges: A:L.167, A:L.167, A:T.218

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

CU.8: 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.9: 6 residues within 4Å: Chain A: H.93, H.140, H.436, H.502 Ligands: CU.11, OXY.14 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.140, A:H.436, A:H.502 CU.10: 6 residues within 4Å: Chain A: H.95, W.136, H.138, H.504 Ligands: CU.11, OXY.14 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.95, A:H.138, A:H.504 CU.11: 8 residues within 4Å: Chain A: H.93, H.95, H.434, H.436 Ligands: CU.9, CU.10, CL.12, OXY.14 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.93, A:H.434

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

CL.12: 8 residues within 4Å: Chain A: H.93, W.94, H.95, G.96, H.434, L.435, H.436 Ligands: CU.11 Ligand excluded by PLIP

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

SO4.13: 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.128, A:R.128 Salt bridges: A:R.128, A:R.130

1 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.14: 11 residues within 4Å: Chain A: H.93, H.95, H.138, H.140, H.434, H.436, H.502, H.504 Ligands: CU.9, CU.10, CU.11 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hakulinen, N. et al., A crystallographic and spectroscopic study on the effect of X-ray radiation on the crystal structure of Melanocarpus albomyces laccase. Biochem.Biophys.Res.Commun. (2006)

Release Date

2006-11-14

Peptides

Laccase-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Laccase-1

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