SMTL ID : 2xu9.1

Crystal structure of Laccase from Thermus thermophilus HB27

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

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

CU.1: 5 residues within 4Å: Chain A: H.370, C.422, I.424, H.427, M.432 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.370, A:C.422, A:H.427 CU.2: 7 residues within 4Å: Chain A: H.72, H.114, H.373, H.375, H.421 Ligands: CU.20, OH.21 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.114, A:H.375, A:H.421 CU.3: 7 residues within 4Å: Chain A: H.72, H.74, W.110, H.112, H.423 Ligands: CU.20, OH.21 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.74, A:H.112, A:H.423 CU.20: 7 residues within 4Å: Chain A: H.72, H.74, H.373, H.375 Ligands: CU.2, CU.3, OH.21 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.72, A:H.373, H2O.6

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

MPD.4: 12 residues within 4Å: Chain A: L.221, A.224, D.225, L.238, L.239, L.240, E.244, R.245, A.246, Y.391, K.395 Ligands: MRD.9 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.221, A:A.224, A:L.240 Hydrogen bonds: A:D.225, A:R.245, A:K.395 MPD.13: 6 residues within 4Å: Chain A: P.5, E.6, F.44, N.183, G.184 Ligands: MRD.17 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.5 Hydrogen bonds: A:E.6, A:G.184 MPD.14: 3 residues within 4Å: Chain A: N.339, G.340, Q.341 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Q.341, A:Q.341, A:Q.341 MPD.15: 4 residues within 4Å: Chain A: K.8, L.21, G.41, P.47 No protein-ligand interaction detected (PLIP) MPD.16: 4 residues within 4Å: Chain A: P.168, W.171, R.430 Ligands: MRD.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.168, A:W.171 Water bridges: A:R.430 MPD.18: 4 residues within 4Å: Chain A: D.216, H.217, P.218 Ligands: MRD.11 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.216, A:D.216

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

MRD.5: 5 residues within 4Å: Chain A: E.104, L.316, W.394, P.411, R.413 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.104, A:L.316, A:P.411 MRD.6: 5 residues within 4Å: Chain A: P.168, M.169, M.172, M.272, M.332 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.168 MRD.7: 3 residues within 4Å: Chain A: K.81, K.415, G.416 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.415 Water bridges: A:G.416 MRD.8: 5 residues within 4Å: Chain A: G.117, W.171, D.429, R.430 Ligands: MPD.16 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.171, A:W.171, A:D.429 Hydrogen bonds: A:R.430 Water bridges: A:R.335, A:D.429 MRD.9: 6 residues within 4Å: Chain A: L.233, V.235, E.237, L.238, P.390 Ligands: MPD.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.233, A:V.235, A:P.390 Water bridges: A:L.239, A:L.239 MRD.10: 4 residues within 4Å: Chain A: E.104, L.105, F.228, S.311 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.104, A:S.311 MRD.11: 4 residues within 4Å: Chain A: P.218, E.234, S.236 Ligands: MPD.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.234 Water bridges: A:E.234, A:E.234 MRD.12: 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.17: 4 residues within 4Å: Chain A: P.2, S.3, P.5 Ligands: MPD.13 No protein-ligand interaction detected (PLIP) MRD.19: 4 residues within 4Å: Chain A: P.121, P.165, H.166, W.171 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.121, A:H.166 Hydrogen bonds: A:H.166, A:H.166

1 x OH: HYDROXIDE ION(Non-covalent)

OH.21: 12 residues within 4Å: Chain A: H.72, H.74, H.112, H.114, H.373, H.375, H.421, H.423, E.428 Ligands: CU.2, CU.3, CU.20 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.423

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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