SMTL ID : 6ze7.1 (1 other biounit)

Chaetomium thermophilum FAD-dependent oxidoreductase in complex with 4-nitrophenol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 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: 9 residues within 4Å: Chain A: T.128, T.130, R.151, S.152, G.153, N.156, D.201, A.202, R.203 No protein-ligand interaction detected (PLIP)

1 x FDA: DIHYDROFLAVINE-ADENINE DINUCLEOTIDE(Non-covalent)

FDA.2: 36 residues within 4Å: Chain A: G.12, G.14, I.15, S.16, I.35, E.36, A.37, W.60, A.81, Q.82, V.83, G.86, G.87, S.88, I.90, N.91, A.92, M.93, V.94, H.230, L.231, V.232, A.268, A.269, G.270, I.277, N.521, A.522, H.523, D.555, I.556, S.566, P.567, M.568 Ligands: NPO.7, FMT.8 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:N.91, A:A.522 Hydrogen bonds: A:I.15, A:S.16, A:S.16, A:S.16, A:A.37, A:A.81, A:V.83, A:G.86, A:G.87, A:S.88, A:N.91, A:A.92, A:V.94, A:V.94, A:V.232, A:V.232, A:A.522, A:I.556, A:S.566, A:M.568 Water bridges: A:G.14, A:G.17, A:T.80, A:A.81, A:A.81, A:G.271, A:A.569

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

NAG.3: 2 residues within 4Å: Chain A: N.72, N.73 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.73 NAG.4: 7 residues within 4Å: Chain A: A.139, G.140, N.141, F.163, E.168, W.171, N.172 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.163, A:E.168 Hydrogen bonds: A:N.141, A:E.168, A:E.168, A:E.168, A:N.172 Water bridges: A:N.175 NAG.5: 5 residues within 4Å: Chain A: F.324, N.333, T.335, Y.336, E.339 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.333, A:Y.336, A:E.339 Water bridges: A:E.339

2 x NPO: P-NITROPHENOL(Non-covalent)

NPO.6: 14 residues within 4Å: Chain A: V.94, L.96, K.190, F.194, I.362, V.364, T.423, Y.435, L.437, N.521, H.523, G.565, S.566 Ligands: FMT.8 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.94, A:L.96, A:I.362, A:Y.435, A:L.437 Hydrogen bonds: A:N.521, A:H.523 NPO.7: 7 residues within 4Å: Chain A: F.53, P.55, I.79, S.520, N.521, A.522 Ligands: FDA.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.79 Hydrogen bonds: A:S.520

3 x FMT: FORMIC ACID(Non-functional Binders)

FMT.8: 7 residues within 4Å: Chain A: V.94, Y.435, N.521, H.523, S.566 Ligands: FDA.2, NPO.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.521 FMT.9: 4 residues within 4Å: Chain A: A.371, P.372, K.373, S.374 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.373, A:S.374, A:S.374 FMT.10: 5 residues within 4Å: Chain A: N.141, T.143, W.171, P.181, V.182 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.141 Water bridges: A:V.182

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.11: 4 residues within 4Å: Chain A: N.322, V.323, F.324, N.326 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.322, A:N.326

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.12: 2 residues within 4Å: Chain A: L.330, T.331 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.331 Water bridges: A:F.53, A:N.337

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.13: 1 residues within 4Å: Chain A: W.56 No protein-ligand interaction detected (PLIP)

3 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.15: 1 residues within 4Å: Chain A: N.141 No protein-ligand interaction detected (PLIP) MG.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x NA: SODIUM ION(Non-functional Binders)

NA.17: 1 residues within 4Å: Chain A: Q.349 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.349, A:Q.349 Water bridges: A:S.133, A:S.133

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Svecova, L. et al., Crystallographic fragment screening-based study of a novel FAD-dependent oxidoreductase from Chaetomium thermophilum. Acta Crystallogr D Struct Biol (2021)

Release Date

2021-05-26

Peptides

FAD-dependent oxidoreductase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

FAD-dependent oxidoreductase

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