SMTL ID : 5afa.1

Crystal structure of Laccase from Thermus thermophilus HB27 complexed with Ag, crystal of the holoenzyme soaked for 30 m in 5 mM AgNO3 at 278 K.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

monomer

Ligands

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

MPD.1: 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.5 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.8: 5 residues within 4Å: Chain A: P.5, E.6, F.44, N.183 Ligands: MRD.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.6, A:F.44 Water bridges: A:E.6 MPD.9: 3 residues within 4Å: Chain A: N.339, G.340, Q.341 No protein-ligand interaction detected (PLIP) MPD.10: 4 residues within 4Å: Chain A: K.8, L.19, G.41, P.47 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.19 MPD.11: 4 residues within 4Å: Chain A: P.168, W.171, R.430 Ligands: MRD.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.168, A:W.171 Hydrogen bonds: A:A.333, A:R.430 Water bridges: A:R.430 MPD.13: 4 residues within 4Å: Chain A: D.216, H.217, P.218 Ligands: MRD.7 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.216

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

MRD.2: 6 residues within 4Å: Chain A: E.104, P.314, L.316, W.394, P.411, R.413 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:E.104, A:P.314, A:L.316, A:W.394, A:P.411 Water bridges: A:E.104 MRD.3: 3 residues within 4Å: Chain A: K.81, K.415, G.416 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.81, A:K.415 MRD.4: 5 residues within 4Å: Chain A: G.117, W.171, D.429, R.430 Ligands: MPD.11 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.171, A:W.171, A:D.429 Hydrogen bonds: A:W.171, A:R.430 MRD.5: 6 residues within 4Å: Chain A: L.233, V.235, E.237, L.238, P.390 Ligands: MPD.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.233, A:V.235, A:P.390 MRD.6: 5 residues within 4Å: Chain A: E.104, L.105, A.106, F.228, S.311 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.104, A:S.311 MRD.7: 3 residues within 4Å: Chain A: P.218, E.234 Ligands: MPD.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.234 Water bridges: A:E.234 MRD.12: 4 residues within 4Å: Chain A: P.2, S.3, P.5 Ligands: MPD.8 No protein-ligand interaction detected (PLIP) MRD.14: 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.165 Hydrogen bonds: A:H.166 Water bridges: A:A.164, A:H.166

3 x AG: SILVER ION(Non-covalent)

AG.15: 5 residues within 4Å: Chain A: M.172, N.173, M.270, M.331, M.368 No protein-ligand interaction detected (PLIP) AG.16: 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 AG.17: 2 residues within 4Å: Chain A: M.169, M.272 No protein-ligand interaction detected (PLIP)

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

CU.18: 7 residues within 4Å: Chain A: H.72, H.114, H.373, H.375, H.421 Ligands: CU.21, OH.22 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.114, A:H.375, A:H.421, OH.22 CU.19: 7 residues within 4Å: Chain A: H.72, H.74, W.110, H.112, H.423 Ligands: CU.21, OH.22 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.74, A:H.112, A:H.423, OH.22 CU.20: 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 CU.21: 7 residues within 4Å: Chain A: H.72, H.74, H.373, H.375 Ligands: CU.18, CU.19, OH.22 4 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:H.72, A:H.373, H2O.4, OH.22

1 x OH: HYDROXIDE ION(Non-covalent)

OH.22: 11 residues within 4Å: Chain A: H.72, H.74, H.112, H.114, H.373, H.375, H.421, H.423 Ligands: CU.18, CU.19, CU.21 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jimenez-Arroyo, N. et al., Structural Function of the Methionine-Rich Beta-Hairpin in the Laccase for T. Thermophilus. To be Published

Release Date

2016-02-17

Peptides

LACCASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

LACCASE

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