SMTL ID : 7zn6.1

Crystal structure of laccase-like multicopper oxidase (LMCO) from Thermothelomyces thermophilus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 7 residues within 4Å: Chain A: D.63, R.64, N.65, W.90, P.91, D.420, Y.595 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.90, A:Y.595 Hydrogen bonds: A:D.420

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 8 residues within 4Å: Chain A: H.15, I.16, L.17, R.18, N.37, P.43, A.44, I.45 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.43, A:I.45 Hydrogen bonds: A:I.16, A:N.37 Water bridges: A:I.16

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 8 residues within 4Å: Chain A: V.185, S.186, P.187, Q.189, Y.333, R.334, G.335, Y.336 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.336 EDO.4: 4 residues within 4Å: Chain A: N.270, D.289, L.356, T.357 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.270, A:D.289, A:T.357 EDO.6: 6 residues within 4Å: Chain A: R.334, Y.336, P.351, T.352, T.353, P.354 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.334, A:T.353 EDO.9: 4 residues within 4Å: Chain A: P.138, Y.139, P.285, L.373 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.138 EDO.10: 4 residues within 4Å: Chain A: E.505, N.508, A.509, A.512 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.508, A:A.509, A:S.513

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 11 residues within 4Å: Chain A: F.169, W.171, R.329, Q.396, L.405, W.407, Y.473, A.476, E.481, H.564, M.567 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.329, A:R.329, A:W.407, A:H.564 GOL.7: 9 residues within 4Å: Chain A: G.72, L.73, S.74, Q.75, D.108, Y.112, S.280, H.491, K.520 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.74, A:S.74, A:D.108, A:S.280 Water bridges: A:H.491

1 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.8: 11 residues within 4Å: Chain A: H.69, H.71, H.115, H.117, H.486, H.488, H.558, H.560 Ligands: CU.11, CU.12, CU.13 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.71, A:H.115, A:H.117, A:H.486, A:H.488, A:H.558, A:H.560

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

CU.11: 5 residues within 4Å: Chain A: H.117, H.486, H.488, H.558 Ligands: OXY.8 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.117, A:H.488, A:H.558 CU.12: 7 residues within 4Å: Chain A: H.69, H.71, F.113, H.115, H.560 Ligands: OXY.8, CU.13 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.71, A:H.115, A:H.560 CU.13: 7 residues within 4Å: Chain A: H.69, H.71, G.72, H.486, H.488 Ligands: OXY.8, CU.12 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.69, A:H.486, H2O.8 CU.14: 6 residues within 4Å: Chain A: H.483, P.484, C.559, I.561, H.564, M.569 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.483, A:C.559, A:H.564

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kosinas, C. et al., Structure-function studies of a novel laccase-like multicopper oxidase from Thermothelomyces thermophila provide insights into its biological role. Acta Crystallogr D Struct Biol (2023)

Release Date

2023-06-28

Peptides

Laccase-like multicopper oxidase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Laccase-like multicopper oxidase 1