SMTL ID : 2xvb.1

Crystal structure of Laccase from Thermus thermophilus HB27 complexed with Hg, crystal of the apoenzyme soaked for 5 min. in 5 mM HgCl2 at 278 K.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

5 x HG: MERCURY (II) ION(Non-covalent)

HG.1: 4 residues within 4Å: Chain A: H.370, C.422, H.427, M.432 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.370, A:C.422, A:H.427 HG.2: 6 residues within 4Å: Chain A: H.72, H.74, W.110, H.112, H.423 Ligands: HG.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.74, A:H.112, A:H.423, H2O.17 HG.3: 5 residues within 4Å: Chain A: H.72, H.74, H.373, H.375 Ligands: HG.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.72, A:H.373 HG.4: 3 residues within 4Å: Chain A: H.114, H.375, H.421 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.114, A:H.375, A:H.421, H2O.17 HG.5: 4 residues within 4Å: Chain A: M.273, M.278, H.280, M.282 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.280

11 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.6: 13 residues within 4Å: Chain A: L.221, A.224, D.225, L.238, L.239, L.240, E.244, R.245, A.246, F.389, Y.391, K.395 Ligands: MPD.17 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.221, A:A.224, A:L.240, A:F.389 Hydrogen bonds: A:D.225, A:R.245, A:K.395 MPD.7: 3 residues within 4Å: Chain A: K.81, K.415, G.416 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.415 Water bridges: A:G.416, A:V.438 MPD.10: 5 residues within 4Å: Chain A: R.52, P.53, E.134, S.135, S.136 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.53 Hydrogen bonds: A:E.134 Water bridges: A:R.52 MPD.11: 6 residues within 4Å: Chain A: G.117, W.171, D.429, R.430 Ligands: MPD.12, MPD.20 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.171, A:W.171, A:D.429 Hydrogen bonds: A:R.430 MPD.12: 5 residues within 4Å: Chain A: P.121, P.165, H.166, W.171 Ligands: MPD.11 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.165, A:W.171 Hydrogen bonds: A:H.166 MPD.13: 4 residues within 4Å: Chain A: K.8, L.21, G.41, P.47 No protein-ligand interaction detected (PLIP) MPD.15: 2 residues within 4Å: Chain A: N.339, Q.341 No protein-ligand interaction detected (PLIP) MPD.17: 6 residues within 4Å: Chain A: L.233, V.235, E.237, L.238, P.390 Ligands: MPD.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.233, A:V.235, A:P.390 Water bridges: A:E.237, A:L.239 MPD.18: 7 residues within 4Å: Chain A: E.104, L.105, A.106, S.135, S.136, F.228, S.311 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.106 Hydrogen bonds: A:E.104, A:S.311 MPD.19: 4 residues within 4Å: Chain A: P.218, E.234, S.236 Ligands: MRD.21 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.234 MPD.20: 4 residues within 4Å: Chain A: P.168, W.171, R.430 Ligands: MPD.11 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.171

6 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.8: 5 residues within 4Å: Chain A: E.104, P.314, L.316, P.411, R.413 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.104, A:P.314, A:L.316, A:P.411 MRD.9: 4 residues within 4Å: Chain A: P.319, V.320, V.321, T.322 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.319 Hydrogen bonds: A:V.320, A:T.322, A:T.322 MRD.14: 7 residues within 4Å: Chain A: P.5, E.6, P.7, F.44, P.45, N.183, G.184 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.5 Hydrogen bonds: A:N.183 Water bridges: A:F.44, A:G.184 MRD.16: 7 residues within 4Å: Chain A: D.266, G.268, D.367, M.368, D.369, K.401, A.402 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:D.266, A:K.401, A:A.402 Hydrogen bonds: A:D.266, A:D.367, A:D.369, A:A.402 MRD.21: 5 residues within 4Å: Chain A: D.216, H.217, P.218, S.236 Ligands: MPD.19 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.216, A:D.216, A:H.217 MRD.22: 6 residues within 4Å: Chain A: P.168, M.169, M.172, M.272, M.331, M.332 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:M.172 Hydrogen bonds: A:M.332

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Serrano-Posada, H. et al., X-Ray-Induced Catalytic Active-Site Reduction of a Multicopper Oxidase: Structural Insights Into the Proton-Relay Mechanism and O2-Reduction States. Acta Crystallogr.,Sect.D (2015)

Release Date

2011-10-26

Peptides

LACCASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

LACCASE

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