SMTL ID : 2yar.1

X-ray induced reduction of laccase from Thermus thermophilus HB27 (87. 5-100.0 percent dose)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

CU.1: 6 residues within 4Å: Chain A: H.72, H.114, H.373, H.375, H.421 Ligands: OH.18 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.375, A:H.421, OH.18 CU.2: 6 residues within 4Å: Chain A: H.72, H.74, W.110, H.112, H.423 Ligands: OH.18 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.74, A:H.112, A:H.423, OH.18 CU.3: 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.19: 6 residues within 4Å: Chain B: H.72, H.114, H.373, H.375, H.421 Ligands: OH.36 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.375, B:H.421 CU.20: 6 residues within 4Å: Chain B: H.72, H.74, W.110, H.112, H.423 Ligands: OH.36 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.74, B:H.112, B:H.423 CU.21: 5 residues within 4Å: Chain B: H.370, C.422, I.424, H.427, M.432 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.370, B:C.422, B:H.427

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

MPD.4: 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: MRD.9 Ligand excluded by PLIP MPD.6: 6 residues within 4Å: Chain A: P.168, M.169, M.172, M.331, M.332 Ligands: MPD.14 Ligand excluded by PLIP MPD.8: 5 residues within 4Å: Chain A: G.117, W.171, D.429, R.430 Ligands: MPD.14 Ligand excluded by PLIP MPD.11: 3 residues within 4Å: Chain A: P.218, E.234 Ligands: MRD.16 Ligand excluded by PLIP MPD.12: 9 residues within 4Å: Chain A: P.319, V.320, V.321, T.322 Chain B: P.319, V.320, V.321, T.322 Ligands: MPD.30 Ligand excluded by PLIP MPD.13: 3 residues within 4Å: Chain A: N.339, G.340, Q.341 Ligand excluded by PLIP MPD.14: 5 residues within 4Å: Chain A: P.168, W.171, R.430 Ligands: MPD.6, MPD.8 Ligand excluded by PLIP MPD.15: 3 residues within 4Å: Chain A: P.2, S.3, P.5 Ligand excluded by PLIP MPD.22: 13 residues within 4Å: Chain B: 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: MRD.27 Ligand excluded by PLIP MPD.24: 6 residues within 4Å: Chain B: P.168, M.169, M.172, M.331, M.332 Ligands: MPD.32 Ligand excluded by PLIP MPD.26: 5 residues within 4Å: Chain B: G.117, W.171, D.429, R.430 Ligands: MPD.32 Ligand excluded by PLIP MPD.29: 3 residues within 4Å: Chain B: P.218, E.234 Ligands: MRD.34 Ligand excluded by PLIP MPD.30: 9 residues within 4Å: Chain A: P.319, V.320, V.321, T.322 Chain B: P.319, V.320, V.321, T.322 Ligands: MPD.12 Ligand excluded by PLIP MPD.31: 3 residues within 4Å: Chain B: N.339, G.340, Q.341 Ligand excluded by PLIP MPD.32: 5 residues within 4Å: Chain B: P.168, W.171, R.430 Ligands: MPD.24, MPD.26 Ligand excluded by PLIP MPD.33: 3 residues within 4Å: Chain B: P.2, S.3, P.5 Ligand excluded by PLIP

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

MRD.5: 4 residues within 4Å: Chain A: E.104, L.316, P.411, R.413 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.104, A:L.316, A:P.411 Water bridges: A:E.104 MRD.7: 2 residues within 4Å: Chain A: K.415, G.416 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.416, A:G.416 MRD.9: 6 residues within 4Å: Chain A: L.233, V.235, E.237, L.238, P.390 Ligands: MPD.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.233, A:V.235 Water bridges: A:L.239 MRD.10: 7 residues within 4Å: Chain A: E.104, L.105, A.106, S.135, S.136, F.228, S.311 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.106 Hydrogen bonds: A:S.311 Water bridges: A:S.136, A:S.136 MRD.16: 4 residues within 4Å: Chain A: H.217, P.218, S.236 Ligands: MPD.11 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.216, A:D.216, A:D.216 MRD.17: 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 MRD.23: 4 residues within 4Å: Chain B: E.104, L.316, P.411, R.413 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.104, B:L.316, B:P.411 MRD.25: 2 residues within 4Å: Chain B: K.415, G.416 2 PLIP interactions: 2 interactions with chain B Water bridges: B:G.416, B:G.416 MRD.27: 6 residues within 4Å: Chain B: L.233, V.235, E.237, L.238, P.390 Ligands: MPD.22 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.233, B:V.235 Water bridges: B:L.239 MRD.28: 7 residues within 4Å: Chain B: E.104, L.105, A.106, S.135, S.136, F.228, S.311 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.106 Hydrogen bonds: B:S.311 Water bridges: B:S.136, B:S.136 MRD.34: 4 residues within 4Å: Chain B: H.217, P.218, S.236 Ligands: MPD.29 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.216, B:D.216 MRD.35: 4 residues within 4Å: Chain B: P.121, P.165, H.166, W.171 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:P.121, B:H.166 Hydrogen bonds: B:H.166, B:H.166

2 x OH: HYDROXIDE ION(Non-covalent)

OH.18: 10 residues within 4Å: Chain A: H.72, H.74, H.112, H.114, H.373, H.375, H.421, H.423 Ligands: CU.1, CU.2 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.112, A:H.114 OH.36: 10 residues within 4Å: Chain B: H.72, H.74, H.112, H.114, H.373, H.375, H.421, H.423 Ligands: CU.19, CU.20 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.375

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

2012-02-29

Peptides

LACCASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

LACCASE

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