SMTL ID : 2xyb.1

CRYSTAL STRUCTURE OF A FULLY FUNCTIONAL LACCASE FROM THE LIGNINOLYTIC FUNGUS PYCNOPORUS CINNABARINUS

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 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

NAG-NAG-BMA-MAN.1: 9 residues within 4Å: Chain A: F.20, R.22, E.23, N.54, M.57, H.153, V.154, A.155, L.158 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.22, A:A.155 Hydrogen bonds: A:A.155 NAG-NAG-BMA-MAN.28: 9 residues within 4Å: Chain B: F.20, R.22, E.23, N.54, M.57, H.153, V.154, A.155, L.158 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:R.22, B:A.155 Hydrogen bonds: B:A.155

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: 5 residues within 4Å: Chain A: N.215, Y.257, S.291, V.292, T.294 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: N.333, T.335, N.336, F.338, T.343 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 5 residues within 4Å: Chain B: N.215, Y.257, S.291, V.292, T.294 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 5 residues within 4Å: Chain B: N.333, T.335, N.336, F.338, T.343 No protein-ligand interaction detected (PLIP)

2 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

NAG-NAG-BMA.4: 5 residues within 4Å: Chain A: P.325, N.327, S.383, P.385, N.434 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.325 Water bridges: A:N.327 NAG-NAG-BMA.31: 5 residues within 4Å: Chain B: P.325, N.327, S.383, P.385, N.434 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.325 Water bridges: B:N.327

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

CU.5: 5 residues within 4Å: Chain A: H.395, C.451, I.453, H.456, F.461 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.395, A:C.451, A:H.456 CU.6: 5 residues within 4Å: Chain A: H.111, H.398, H.400, H.450 Ligands: PER.9 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.111, A:H.400, A:H.450 CU.7: 7 residues within 4Å: Chain A: H.64, H.66, W.107, H.109, H.452 Ligands: CU.8, PER.9 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.66, A:H.109, A:H.452 CU.8: 6 residues within 4Å: Chain A: H.64, H.66, H.398, H.400 Ligands: CU.7, PER.9 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.64, A:H.398, H2O.11 CU.32: 5 residues within 4Å: Chain B: H.395, C.451, I.453, H.456, F.461 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.395, B:C.451, B:H.456 CU.33: 5 residues within 4Å: Chain B: H.111, H.398, H.400, H.450 Ligands: PER.36 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.111, B:H.400, B:H.450 CU.34: 7 residues within 4Å: Chain B: H.64, H.66, W.107, H.109, H.452 Ligands: CU.35, PER.36 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.66, B:H.109, B:H.452 CU.35: 6 residues within 4Å: Chain B: H.64, H.66, H.398, H.400 Ligands: CU.34, PER.36 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.64, B:H.398, H2O.38

2 x PER: PEROXIDE ION(Non-covalent)

PER.9: 11 residues within 4Å: Chain A: H.64, H.66, H.109, H.111, H.398, H.400, H.450, H.452 Ligands: CU.6, CU.7, CU.8 No protein-ligand interaction detected (PLIP) PER.36: 11 residues within 4Å: Chain B: H.64, H.66, H.109, H.111, H.398, H.400, H.450, H.452 Ligands: CU.33, CU.34, CU.35 No protein-ligand interaction detected (PLIP)

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

NAG.10: 1 residues within 4Å: Chain A: N.377 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.377 NAG.37: 1 residues within 4Å: Chain B: N.377 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.377

2 x AS8: ACETYLSULFATE(Non-covalent)

AS8.11: 7 residues within 4Å: Chain A: F.162, P.163, D.206, F.265, P.391, G.392, H.456 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.162 Hydrogen bonds: A:D.206 Salt bridges: A:H.456, A:H.456 AS8.38: 7 residues within 4Å: Chain B: F.162, P.163, D.206, F.265, P.391, G.392, H.456 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.162 Hydrogen bonds: B:D.206 Salt bridges: B:H.456, B:H.456

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.12: 5 residues within 4Å: Chain A: F.69, H.402, A.403, N.442 Ligands: ZN.19 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.69 Hydrogen bonds: A:A.403, A:N.442 Salt bridges: A:H.402 ACT.39: 5 residues within 4Å: Chain B: F.69, H.402, A.403, N.442 Ligands: ZN.46 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.69 Hydrogen bonds: B:A.403 Salt bridges: B:H.402

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

SO4.13: 4 residues within 4Å: Chain A: G.193, R.195, D.249, S.251 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.249 Salt bridges: A:R.195 SO4.14: 4 residues within 4Å: Chain A: S.376, D.468, D.471 Ligands: ZN.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.376, A:S.376 SO4.40: 4 residues within 4Å: Chain B: G.193, R.195, D.249, S.251 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.249 Salt bridges: B:R.195 SO4.41: 4 residues within 4Å: Chain B: S.376, D.468, D.471 Ligands: ZN.48 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.376

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.15: 7 residues within 4Å: Chain A: A.80, H.111, L.112, S.113, P.346, F.448, L.457 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.111, A:S.113 GOL.16: 7 residues within 4Å: Chain A: S.212, I.213, N.215, H.216, D.234, Q.293, T.294 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:H.216, A:H.216, A:T.294, A:T.294 Water bridges: A:S.212, A:D.214, A:N.215, A:Q.293 GOL.17: 6 residues within 4Å: Chain A: N.215, H.216, T.217, D.249, S.251, Q.252 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.217, A:T.217, A:S.251 Water bridges: A:S.251 GOL.18: 8 residues within 4Å: Chain A: Y.127, D.128, P.129, D.131, A.134, Y.137, D.140, R.199 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.131, A:Y.137, A:D.140, A:D.140, A:R.199 Water bridges: A:D.128 GOL.42: 7 residues within 4Å: Chain B: A.80, H.111, L.112, S.113, P.346, F.448, L.457 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.111, B:H.111, B:S.113 GOL.43: 7 residues within 4Å: Chain B: S.212, I.213, N.215, H.216, D.234, Q.293, T.294 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:H.216, B:H.216, B:T.294, B:T.294 Water bridges: B:S.212, B:N.215, B:Q.293 GOL.44: 6 residues within 4Å: Chain B: N.215, H.216, T.217, D.249, S.251, Q.252 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.217, B:T.217, B:S.251 Water bridges: B:S.251 GOL.45: 8 residues within 4Å: Chain B: Y.127, D.128, P.129, D.131, A.134, Y.137, D.140, R.199 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.131, B:D.140, B:R.199 Water bridges: B:D.128, B:D.131

16 x ZN: ZINC ION(Non-covalent)

ZN.19: 5 residues within 4Å: Chain A: G.401, H.402, E.440, N.442 Ligands: ACT.12 4 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:H.402, H2O.5, H2O.6, ACT.12 ZN.20: 1 residues within 4Å: Chain A: E.23 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.23, H2O.2, H2O.2 ZN.21: 3 residues within 4Å: Chain A: D.468, D.471 Ligands: SO4.14 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.468, A:D.471, H2O.18 ZN.22: 2 residues within 4Å: Chain A: H.342, E.368 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.342, A:E.368, H2O.1, H2O.17, H2O.19 ZN.23: 1 residues within 4Å: Chain A: H.306 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.306, H2O.9, H2O.19, H2O.19, H2O.22 ZN.24: 1 residues within 4Å: Chain A: H.91 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.91, H2O.15, H2O.16, H2O.17, H2O.18 ZN.25: 1 residues within 4Å: Chain A: H.55 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.55, H2O.10, H2O.18, H2O.21, H2O.26 ZN.26: 1 residues within 4Å: Chain A: D.418 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.418, H2O.16, H2O.18, H2O.19 ZN.46: 5 residues within 4Å: Chain B: G.401, H.402, E.440, N.442 Ligands: ACT.39 4 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:H.402, H2O.32, H2O.33, ACT.39 ZN.47: 1 residues within 4Å: Chain B: E.23 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.23, H2O.29, H2O.29 ZN.48: 3 residues within 4Å: Chain B: D.468, D.471 Ligands: SO4.41 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.468, B:D.471, H2O.46 ZN.49: 2 residues within 4Å: Chain B: H.342, E.368 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.342, B:E.368, H2O.29, H2O.45, H2O.46 ZN.50: 1 residues within 4Å: Chain B: H.306 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:H.306, H2O.36, H2O.46, H2O.47, H2O.49 ZN.51: 1 residues within 4Å: Chain B: H.91 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:H.91, H2O.43, H2O.44, H2O.45, H2O.46 ZN.52: 1 residues within 4Å: Chain B: H.55 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:H.55, H2O.37, H2O.45, H2O.48, H2O.53 ZN.53: 1 residues within 4Å: Chain B: D.418 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.418, H2O.43, H2O.46, H2O.47

2 x NA: SODIUM ION(Non-functional Binders)

NA.27: 4 residues within 4Å: Chain A: N.331, F.332, N.389 Chain B: G.266 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.331, A:N.389 NA.54: 4 residues within 4Å: Chain A: G.266 Chain B: N.331, F.332, N.389 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.331, A:G.266

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Piontek, K. et al., Substrate Binding and Copper Geometry in Laccases. To be Published

Release Date

2011-11-30

Peptides

LACCASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

LACCASE