SMTL ID : 2yaq.1

X-ray induced reduction of laccase from Thermus thermophilus HB27 (75. 0-87.5 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: 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: 6 residues within 4Å: Chain A: H.72, H.74, W.110, H.112, H.423 Ligands: OH.20 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.74, A:H.112, A:H.423, OH.20 CU.3: 6 residues within 4Å: Chain A: H.72, H.114, H.373, H.375, H.421 Ligands: OH.20 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.375, A:H.421, OH.20 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.74, W.110, H.112, H.423 Ligands: OH.40 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.74, B:H.112, B:H.423 CU.23: 6 residues within 4Å: Chain B: H.72, H.114, H.373, H.375, H.421 Ligands: OH.40 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.375, B:H.421

14 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 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.224, A:L.240, A:F.389 Hydrogen bonds: A:D.225, A:R.245, A:K.395 MPD.8: 4 residues within 4Å: Chain A: G.117, W.171, D.429, R.430 5 PLIP interactions: 5 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 MPD.10: 5 residues within 4Å: Chain A: E.104, L.105, S.136, F.228, S.311 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.104, A:S.311 MPD.14: 3 residues within 4Å: Chain A: N.339, G.340, Q.341 No protein-ligand interaction detected (PLIP) MPD.15: 4 residues within 4Å: Chain A: K.8, L.21, G.41, P.47 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.8, A:L.21, A:P.47 MPD.16: 4 residues within 4Å: Chain A: P.168, W.171, R.430 Ligands: MRD.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.168, A:W.171 Water bridges: A:A.333, A:R.430 MPD.17: 4 residues within 4Å: Chain A: P.2, S.3, P.5 Ligands: MRD.13 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.5 MPD.24: 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.29 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:A.224, B:L.240, B:F.389 Hydrogen bonds: B:D.225, B:R.245, B:Y.391, B:K.395 MPD.28: 4 residues within 4Å: Chain B: G.117, W.171, D.429, R.430 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.171, B:W.171, B:D.429 Hydrogen bonds: B:R.430 Water bridges: B:R.335 MPD.30: 5 residues within 4Å: Chain B: E.104, L.105, S.136, F.228, S.311 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.104, B:S.311 MPD.34: 3 residues within 4Å: Chain B: N.339, G.340, Q.341 No protein-ligand interaction detected (PLIP) MPD.35: 4 residues within 4Å: Chain B: K.8, L.21, G.41, P.47 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.8, B:L.21, B:P.47 MPD.36: 4 residues within 4Å: Chain B: P.168, W.171, R.430 Ligands: MRD.26 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:P.168, B:W.171 Water bridges: B:A.333, B:R.430 MPD.37: 4 residues within 4Å: Chain B: P.2, S.3, P.5 Ligands: MRD.33 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.5

18 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 Ligand excluded by PLIP MRD.6: 5 residues within 4Å: Chain A: P.168, M.169, M.272, M.332 Ligands: MPD.16 Ligand excluded by PLIP MRD.7: 2 residues within 4Å: Chain A: K.81, G.416 Ligand excluded by PLIP MRD.9: 6 residues within 4Å: Chain A: L.233, V.235, E.237, L.238, P.390 Ligands: MPD.4 Ligand excluded by PLIP MRD.11: 4 residues within 4Å: Chain A: P.218, E.234, S.236 Ligands: MRD.18 Ligand excluded by PLIP MRD.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: MRD.32 Ligand excluded by PLIP MRD.13: 8 residues within 4Å: Chain A: P.5, E.6, P.7, F.44, P.45, N.183, G.184 Ligands: MPD.17 Ligand excluded by PLIP MRD.18: 5 residues within 4Å: Chain A: D.216, H.217, P.218, S.236 Ligands: MRD.11 Ligand excluded by PLIP MRD.19: 4 residues within 4Å: Chain A: P.121, P.165, H.166, W.171 Ligand excluded by PLIP MRD.25: 4 residues within 4Å: Chain B: E.104, L.316, P.411, R.413 Ligand excluded by PLIP MRD.26: 5 residues within 4Å: Chain B: P.168, M.169, M.272, M.332 Ligands: MPD.36 Ligand excluded by PLIP MRD.27: 2 residues within 4Å: Chain B: K.81, G.416 Ligand excluded by PLIP MRD.29: 6 residues within 4Å: Chain B: L.233, V.235, E.237, L.238, P.390 Ligands: MPD.24 Ligand excluded by PLIP MRD.31: 4 residues within 4Å: Chain B: P.218, E.234, S.236 Ligands: MRD.38 Ligand excluded by PLIP MRD.32: 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: MRD.12 Ligand excluded by PLIP MRD.33: 8 residues within 4Å: Chain B: P.5, E.6, P.7, F.44, P.45, N.183, G.184 Ligands: MPD.37 Ligand excluded by PLIP MRD.38: 5 residues within 4Å: Chain B: D.216, H.217, P.218, S.236 Ligands: MRD.31 Ligand excluded by PLIP MRD.39: 4 residues within 4Å: Chain B: P.121, P.165, H.166, W.171 Ligand excluded by PLIP

2 x OH: HYDROXIDE ION(Non-covalent)

OH.20: 10 residues within 4Å: Chain A: H.72, H.74, H.112, H.114, H.373, H.375, H.421, H.423 Ligands: CU.2, CU.3 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.112, A:H.114 OH.40: 10 residues within 4Å: Chain B: H.72, H.74, H.112, H.114, H.373, H.375, H.421, H.423 Ligands: CU.22, CU.23 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.421

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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