SMTL ID : 2yaf.1

X-ray induced reduction of laccase from Thermus thermophilus HB27 (12. 5-25.0 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.74, W.110, H.112, H.423 Ligands: OH.19 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.74, A:H.112, A:H.423 CU.2: 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.3: 6 residues within 4Å: Chain A: H.72, H.114, H.373, H.375, H.421 Ligands: OH.19 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.375, A:H.421, OH.19 CU.20: 6 residues within 4Å: Chain B: H.72, H.74, W.110, H.112, H.423 Ligands: OH.38 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 CU.22: 6 residues within 4Å: Chain B: H.72, H.114, H.373, H.375, H.421 Ligands: OH.38 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.375, B:H.421

18 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: MPD.9 Ligand excluded by PLIP MPD.8: 4 residues within 4Å: Chain A: G.117, W.171, D.429, R.430 Ligand excluded by PLIP MPD.9: 6 residues within 4Å: Chain A: L.233, V.235, E.237, L.238, P.390 Ligands: MPD.4 Ligand excluded by PLIP MPD.10: 5 residues within 4Å: Chain A: E.104, L.105, S.135, F.228, S.311 Ligand excluded by PLIP MPD.12: 8 residues within 4Å: Chain A: P.319, V.320, V.321, T.322 Chain B: P.319, V.320, T.322 Ligands: MPD.31 Ligand excluded by PLIP MPD.13: 2 residues within 4Å: Chain A: N.339, Q.341 Ligand excluded by PLIP MPD.14: 4 residues within 4Å: Chain A: K.8, L.19, G.41, P.47 Ligand excluded by PLIP MPD.15: 5 residues within 4Å: Chain A: P.168, W.171, M.332, R.430 Ligands: MRD.6 Ligand excluded by PLIP MPD.16: 2 residues within 4Å: Chain A: S.3, P.5 Ligand excluded by PLIP MPD.23: 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: MPD.28 Ligand excluded by PLIP MPD.27: 4 residues within 4Å: Chain B: G.117, W.171, D.429, R.430 Ligand excluded by PLIP MPD.28: 6 residues within 4Å: Chain B: L.233, V.235, E.237, L.238, P.390 Ligands: MPD.23 Ligand excluded by PLIP MPD.29: 5 residues within 4Å: Chain B: E.104, L.105, S.135, F.228, S.311 Ligand excluded by PLIP MPD.31: 8 residues within 4Å: Chain A: P.319, V.320, T.322 Chain B: P.319, V.320, V.321, T.322 Ligands: MPD.12 Ligand excluded by PLIP MPD.32: 2 residues within 4Å: Chain B: N.339, Q.341 Ligand excluded by PLIP MPD.33: 4 residues within 4Å: Chain B: K.8, L.19, G.41, P.47 Ligand excluded by PLIP MPD.34: 5 residues within 4Å: Chain B: P.168, W.171, M.332, R.430 Ligands: MRD.25 Ligand excluded by PLIP MPD.35: 2 residues within 4Å: Chain B: 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 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.104, A:L.316, A:P.411 MRD.6: 6 residues within 4Å: Chain A: P.168, M.169, M.172, M.331, M.332 Ligands: MPD.15 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.168 Hydrogen bonds: A:M.332 Water bridges: A:M.169 MRD.7: 2 residues within 4Å: Chain A: K.415, G.416 No protein-ligand interaction detected (PLIP) MRD.11: 3 residues within 4Å: Chain A: P.218, E.234 Ligands: MRD.17 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.218 Hydrogen bonds: A:E.234, A:E.234 Water bridges: A:E.234, A:E.234 MRD.17: 4 residues within 4Å: Chain A: D.216, H.217, P.218 Ligands: MRD.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.216 Water bridges: A:D.216, A:D.216 MRD.18: 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.24: 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: 6 residues within 4Å: Chain B: P.168, M.169, M.172, M.331, M.332 Ligands: MPD.34 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.168 Hydrogen bonds: B:M.332 Water bridges: B:M.169 MRD.26: 2 residues within 4Å: Chain B: K.415, G.416 No protein-ligand interaction detected (PLIP) MRD.30: 3 residues within 4Å: Chain B: P.218, E.234 Ligands: MRD.36 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:P.218 Hydrogen bonds: B:E.234 Water bridges: B:E.234, B:E.234 MRD.36: 4 residues within 4Å: Chain B: D.216, H.217, P.218 Ligands: MRD.30 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.216 Water bridges: B:D.216 MRD.37: 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.19: 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.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.428 OH.38: 10 residues within 4Å: Chain B: H.72, H.74, H.112, H.114, H.373, H.375, H.421, H.423 Ligands: CU.20, CU.22 No protein-ligand interaction detected (PLIP)

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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