SMTL ID : 3dkh.1 (1 other biounit)

L559A mutant of Melanocarpus albomyces laccase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

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: 12 residues within 4Å: Chain A: 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 A Hydrogen bonds: A:R.178, A:R.178, A:D.182, A:D.181, A:D.182, A:D.182 Water bridges: A:R.178, A:A.180 Hydrophobic interactions: A:K.56, A:A.179

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

4 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: 11 residues within 4Å: Chain A: Y.214, W.287, N.289, T.291, H.305, A.307, L.319, E.323, G.324, T.325, P.326 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.287, A:L.319 Hydrogen bonds: A:E.323 Water bridges: A:Y.214, A:Y.214 NAG-NAG-BMA.6: 13 residues within 4Å: Chain B: E.42, E.55, K.56, M.58, T.87, N.88, R.178, A.179, D.181, D.182, N.550, Y.552, P.553 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.178, B:D.181, B:D.182, B:D.182 Hydrophobic interactions: B:K.56, B:A.179 Water bridges: B:D.181, B:Y.552 NAG-NAG-BMA.7: 6 residues within 4Å: Chain B: N.216, T.218, I.309, H.311, G.314, G.317 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.314 NAG-NAG-BMA.8: 8 residues within 4Å: Chain B: W.287, N.289, T.291, H.305, A.307, E.323, T.325, P.326 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.323 Hydrophobic interactions: B:W.287 Hydrogen bonds: B:E.323

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

NAG.10: 3 residues within 4Å: Chain A: N.39, T.41, N.84 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.84 Water bridges: A:N.84, A:N.84 NAG.11: 3 residues within 4Å: Chain A: K.386, Y.391, N.396 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.386, A:Y.391, A:Y.391, A:N.396 NAG.20: 3 residues within 4Å: Chain B: N.39, T.41, N.84 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.84 Water bridges: B:N.84 NAG.21: 3 residues within 4Å: Chain B: K.386, Y.391, N.396 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.386, B:N.396 NAG.22: 5 residues within 4Å: Chain B: L.167, V.169, F.170, N.201, V.217 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.217 Hydrogen bonds: B:V.169, B:N.201 Water bridges: B:L.167 NAG.23: 4 residues within 4Å: Chain B: N.244, R.281, A.282, Y.286 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.281, B:Y.286

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

CU.12: 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.13: 4 residues within 4Å: Chain A: H.140, H.436, H.502 Ligands: OXY.19 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.140, A:H.436, A:H.502 CU.14: 5 residues within 4Å: Chain A: H.95, W.136, H.138, H.504 Ligands: OXY.19 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.95, A:H.138, A:H.504 CU.15: 5 residues within 4Å: Chain A: H.93, H.434, H.436 Ligands: CL.16, OXY.19 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.93, A:H.434 CU.24: 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.25: 4 residues within 4Å: Chain B: H.140, H.436, H.502 Ligands: OXY.29 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.140, B:H.436, B:H.502 CU.26: 5 residues within 4Å: Chain B: H.95, W.136, H.138, H.504 Ligands: OXY.29 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.95, B:H.138, B:H.504 CU.27: 5 residues within 4Å: Chain B: H.93, H.95, H.434, H.436 Ligands: OXY.29 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.93, B:H.434

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

CL.16: 8 residues within 4Å: Chain A: H.93, W.94, H.95, G.96, I.97, H.434, L.435 Ligands: CU.15 Ligand excluded by PLIP

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

SO4.17: 1 residues within 4Å: Chain A: R.492 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.492 Salt bridges: A:R.492 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 SO4.28: 1 residues within 4Å: Chain B: R.492 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.492 Salt bridges: B:R.492

2 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.19: 11 residues within 4Å: Chain A: H.93, H.95, H.138, H.140, H.434, H.436, H.502, H.504 Ligands: CU.13, CU.14, CU.15 No protein-ligand interaction detected (PLIP) OXY.29: 11 residues within 4Å: Chain B: H.93, H.95, H.138, H.140, H.434, H.436, H.502, H.504 Ligands: CU.25, CU.26, CU.27 1 PLIP interactions: 1 interactions with chain B Water bridges: B:H.504

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.30: 4 residues within 4Å: Chain A: A.191, F.371, F.427 Chain B: F.427 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Andberg, M. et al., Essential role of the C-terminus in Melanocarpus albomyces laccase for enzyme production, catalytic properties and structure. Febs J. (2009)

Release Date

2009-07-07

Peptides

Laccase-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Laccase-1

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