SMTL ID : 2yap.1

X-ray induced reduction of laccase from Thermus thermophilus HB27 (62. 5-75.0 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: 5 residues within 4Å: Chain A: H.72, H.74, W.110, H.112, H.423 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: 5 residues within 4Å: Chain A: H.72, H.114, H.373, H.375, H.421 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.375, A:H.421 CU.20: 5 residues within 4Å: Chain B: H.72, H.74, W.110, H.112, H.423 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: 5 residues within 4Å: Chain B: H.72, H.114, H.373, H.375, H.421 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.375, B:H.421

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.8: 4 residues within 4Å: Chain A: G.117, W.171, D.429, R.430 Ligand excluded by PLIP MPD.10: 5 residues within 4Å: Chain A: E.104, L.105, S.136, F.228, S.311 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.31 Ligand excluded by PLIP MPD.13: 8 residues within 4Å: Chain A: P.5, E.6, P.7, F.44, P.45, N.183, G.184, A.185 Ligand excluded by PLIP MPD.14: 3 residues within 4Å: Chain A: N.339, G.340, Q.341 Ligand excluded by PLIP MPD.15: 4 residues within 4Å: Chain A: K.8, L.21, G.41, P.47 Ligand excluded by PLIP MPD.17: 3 residues within 4Å: Chain A: P.2, 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: MRD.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.29: 5 residues within 4Å: Chain B: E.104, L.105, S.136, F.228, S.311 Ligand excluded by PLIP MPD.31: 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.32: 8 residues within 4Å: Chain B: P.5, E.6, P.7, F.44, P.45, N.183, G.184, A.185 Ligand excluded by PLIP MPD.33: 3 residues within 4Å: Chain B: N.339, G.340, Q.341 Ligand excluded by PLIP MPD.34: 4 residues within 4Å: Chain B: K.8, L.21, G.41, P.47 Ligand excluded by PLIP MPD.36: 3 residues within 4Å: Chain B: P.2, S.3, P.5 Ligand excluded by PLIP

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

MRD.5: 5 residues within 4Å: Chain A: E.104, P.314, L.316, P.411, R.413 Ligand excluded by PLIP MRD.6: 6 residues within 4Å: Chain A: P.168, M.169, M.272, M.331, M.332 Ligands: MRD.16 Ligand excluded by PLIP MRD.7: 2 residues within 4Å: Chain A: K.81, K.415 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.16: 6 residues within 4Å: Chain A: P.168, W.171, M.332, A.333, R.430 Ligands: MRD.6 Ligand excluded by PLIP MRD.18: 4 residues within 4Å: Chain A: D.216, H.217, P.218 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.24: 5 residues within 4Å: Chain B: E.104, P.314, L.316, P.411, R.413 Ligand excluded by PLIP MRD.25: 6 residues within 4Å: Chain B: P.168, M.169, M.272, M.331, M.332 Ligands: MRD.35 Ligand excluded by PLIP MRD.26: 2 residues within 4Å: Chain B: K.81, K.415 Ligand excluded by PLIP MRD.28: 6 residues within 4Å: Chain B: L.233, V.235, E.237, L.238, P.390 Ligands: MPD.23 Ligand excluded by PLIP MRD.30: 4 residues within 4Å: Chain B: P.218, E.234, S.236 Ligands: MRD.37 Ligand excluded by PLIP MRD.35: 6 residues within 4Å: Chain B: P.168, W.171, M.332, A.333, R.430 Ligands: MRD.25 Ligand excluded by PLIP MRD.37: 4 residues within 4Å: Chain B: D.216, H.217, P.218 Ligands: MRD.30 Ligand excluded by PLIP MRD.38: 4 residues within 4Å: Chain B: P.121, P.165, H.166, W.171 Ligand excluded by 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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