SMTL ID : 5k84.1

Crystal structure of laccase from Thermus thermophilus HB27 (sodium nitrate 10 min)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

monomer

Ligands

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

CU.1: 5 residues within 4Å: Chain A: H.72, H.114, H.373, H.375, H.421 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.114, A:H.375, A:H.421 CU.2: 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.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

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

MPD.4: 12 residues within 4Å: Chain A: L.221, A.224, D.225, L.239, L.240, E.244, R.245, A.246, F.389, Y.391, K.395 Ligands: MPD.11 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.221, A:A.224, A:L.240, A:F.389 Hydrogen bonds: A:D.225, A:R.245, A:Y.391, A:K.395 MPD.5: 6 residues within 4Å: Chain A: G.117, W.171, D.429, R.430 Ligands: MPD.10, MPD.12 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.171, A:D.429 Hydrogen bonds: A:R.430 Water bridges: A:R.335 MPD.6: 4 residues within 4Å: Chain A: E.104, L.105, F.228, S.311 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.104, A:S.311 MPD.7: 5 residues within 4Å: Chain A: E.104, L.316, W.394, P.411, R.413 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.104, A:L.316, A:W.394 Water bridges: A:L.412 MPD.8: 4 residues within 4Å: Chain A: P.168, M.272, M.332 Ligands: MPD.12 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.168 Water bridges: A:M.169 MPD.9: 4 residues within 4Å: Chain A: P.5, F.44, N.183, A.185 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.5, A:A.185 MPD.10: 5 residues within 4Å: Chain A: P.121, P.165, H.166, W.171 Ligands: MPD.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.121, A:P.165, A:W.171 MPD.11: 6 residues within 4Å: Chain A: L.233, V.235, E.237, L.238, P.390 Ligands: MPD.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.233, A:L.238, A:P.390 Water bridges: A:E.237 MPD.12: 5 residues within 4Å: Chain A: P.168, W.171, R.430 Ligands: MPD.5, MPD.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.171 Hydrogen bonds: A:R.430 Water bridges: A:R.335, A:R.430 MPD.13: 2 residues within 4Å: Chain A: K.81, G.416 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.81 MPD.14: 3 residues within 4Å: Chain A: P.218, E.234, S.236 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.218 MPD.15: 2 residues within 4Å: Chain A: N.339, Q.341 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.341 Hydrogen bonds: A:N.339 MPD.16: 5 residues within 4Å: Chain A: K.8, L.19, K.20, L.21, G.41 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.21 Hydrogen bonds: A:K.8, A:K.20 MPD.17: 4 residues within 4Å: Chain A: P.319, V.320, V.321, T.322 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.319 Hydrogen bonds: A:V.320, A:T.322

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Diaz-Vilchis, A. et al., Preserving metallic sites affected by radiation damage: the CuT2 case in Thermus thermophilus multicopper oxidase. To be Published

Release Date

2017-06-07

Peptides

Laccase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Laccase

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