SMTL ID : 2q9o.1

Near-atomic resolution structure of a Melanocarpus albomyces laccase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

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.1: 6 residues within 4Å: Chain A: P.355, D.356, T.358, L.359, N.376, V.406 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.356 NAG-NAG.3: 9 residues within 4Å: Chain A: N.216, T.218, I.309, H.311, A.313, G.314, A.315, 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.7: 8 residues within 4Å: Chain B: N.216, T.218, I.309, H.311, A.313, G.314, G.317, G.318 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.314 NAG-NAG.8: 11 residues within 4Å: Chain B: Y.214, W.287, N.289, T.291, H.305, A.307, L.319, E.323, G.324, T.325, P.326 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.287, B:L.319 Water bridges: B:Y.214, B:Y.214 NAG-NAG.9: 6 residues within 4Å: Chain B: P.355, D.356, T.358, L.359, N.376, V.406 No protein-ligand interaction detected (PLIP)

3 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(Post Translational Modification)

NAG-NAG-MAN.2: 15 residues within 4Å: Chain A: E.42, E.55, K.56, M.58, T.87, N.88, F.141, A.179, D.181, D.182, H.185, W.384, N.550, Y.552, P.553 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.179 Hydrogen bonds: A:D.181, A:D.182, A:D.182 Water bridges: A:E.55, A:D.181 NAG-NAG-MAN.4: 9 residues within 4Å: Chain A: Y.214, W.287, N.289, T.291, H.305, A.307, E.323, T.325, P.326 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.287 Water bridges: A:Y.214, A:Y.214 NAG-NAG-MAN.6: 15 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, H.185, W.384, N.550, Y.552, P.553 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.179 Hydrogen bonds: B:D.181, B:D.182, B:D.182 Water bridges: B:E.55, B:D.181

2 x NAG- NAG- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG-NAG-MAN-MAN-MAN.5: 10 residues within 4Å: Chain A: P.7, R.10, D.166, L.167, G.168, V.169, F.170, N.201, V.217, L.227 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.10, A:R.10 NAG-NAG-MAN-MAN-MAN.10: 10 residues within 4Å: Chain B: P.7, R.10, D.166, L.167, G.168, V.169, F.170, N.201, V.217, L.227 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.10, B:R.10 Water bridges: B:N.5, B:D.164

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

NAG.11: 4 residues within 4Å: Chain A: N.39, T.41, 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.39 NAG.12: 4 residues within 4Å: Chain A: K.386, Y.391, N.396, S.398 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.386, A:Y.391, A:Y.391, A:N.396 Water bridges: A:N.396 NAG.13: 3 residues within 4Å: Chain A: N.244, D.284, Y.286 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.286 Water bridges: A:Y.286, A:Y.286, A:D.322 NAG.24: 4 residues within 4Å: Chain B: N.39, T.41, I.82, N.84 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.82 Hydrogen bonds: B:N.84 Water bridges: B:N.39 NAG.25: 3 residues within 4Å: Chain B: K.386, Y.391, N.396 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.386 Water bridges: B:N.396, B:S.398, B:S.398

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

CU.14: 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.15: 6 residues within 4Å: Chain A: H.140, H.434, H.436, H.502 Ligands: CU.17, OXY.22 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.140, A:H.436, A:H.502 CU.16: 6 residues within 4Å: Chain A: H.95, W.136, H.138, H.504 Ligands: CU.17, OXY.22 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.95, A:H.138, A:H.504 CU.17: 8 residues within 4Å: Chain A: H.93, H.95, H.434, H.436 Ligands: CU.15, CU.16, CL.18, OXY.22 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.93, A:H.434 CU.26: 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.27: 6 residues within 4Å: Chain B: H.140, H.434, H.436, H.502 Ligands: CU.29, OXY.33 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.140, B:H.436, B:H.502 CU.28: 7 residues within 4Å: Chain B: H.93, H.95, W.136, H.138, H.504 Ligands: CU.29, OXY.33 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.95, B:H.138, B:H.504 CU.29: 8 residues within 4Å: Chain B: H.93, H.95, H.434, H.436 Ligands: CU.27, CU.28, CL.30, OXY.33 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.18: 7 residues within 4Å: Chain A: H.93, W.94, H.95, G.96, H.434, H.436 Ligands: CU.17 Ligand excluded by PLIP CL.30: 8 residues within 4Å: Chain B: H.93, W.94, H.95, G.96, H.434, L.435, H.436 Ligands: CU.29 Ligand excluded by PLIP

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

SO4.19: 1 residues within 4Å: Chain A: R.492 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.492, A:R.492 Salt bridges: A:R.492 SO4.20: 2 residues within 4Å: Chain A: R.520, R.527 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.527, A:R.527, A:R.527 Salt bridges: A:R.520, A:R.527 SO4.21: 3 residues within 4Å: Chain A: P.447, D.448, R.467 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.448 Water bridges: A:R.445, A:D.448, A:D.448, A:R.467, A:R.467 Salt bridges: A:R.467 SO4.31: 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 SO4.32: 3 residues within 4Å: Chain B: P.447, D.448, R.467 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.448 Water bridges: B:R.467, B:R.467 Salt bridges: B:R.467

2 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.22: 11 residues within 4Å: Chain A: H.93, H.95, H.138, H.140, H.434, H.436, H.502, H.504 Ligands: CU.15, CU.16, CU.17 No protein-ligand interaction detected (PLIP) OXY.33: 11 residues within 4Å: Chain B: H.93, H.95, H.138, H.140, H.434, H.436, H.502, H.504 Ligands: CU.27, CU.28, CU.29 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.23: 6 residues within 4Å: Chain A: A.191, P.192, L.363, F.371, W.373, F.427 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.373 GOL.34: 4 residues within 4Å: Chain B: A.191, P.192, F.371, F.427 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hakulinen, N. et al., A near atomic resolution structure of a Melanocarpus albomyces laccase. J.Struct.Biol. (2008)

Release Date

2008-03-25

Peptides

Laccase-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Laccase-1

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