SMTL ID : 8dsv.1

The structure of NicA2 in complex with N-methylmyosmine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

FDA.1: 40 residues within 4Å: Chain A: V.9, G.10, G.11, G.12, F.13, A.14, G.15, L.32, E.33, A.34, R.35, G.39, G.40, R.41, T.42, F.54, G.55, G.56, A.57, W.58, V.227, P.228, V.229, T.257, V.258, P.259, T.262, I.266, K.290, W.367, F.372, A.376, W.377, G.402, A.403, A.411, N.412, I.413, A.416 Ligands: PG4.3 35 PLIP interactions: 35 interactions with chain A Hydrophobic interactions: A:W.367, A:A.376, A:W.377, A:W.377 Hydrogen bonds: A:G.11, A:G.12, A:F.13, A:A.14, A:E.33, A:A.34, A:R.35, A:G.39, A:G.40, A:R.41, A:G.56, A:A.57, A:W.58, A:W.58, A:V.229, A:V.229, A:A.403, A:N.412, A:N.412, A:I.413 Water bridges: A:G.15, A:R.35, A:R.41, A:R.41, A:T.42, A:T.42, A:D.414 Salt bridges: A:R.41, A:R.41 pi-Stacking: A:F.372, A:W.377 FDA.4: 44 residues within 4Å: Chain B: V.9, G.10, G.11, G.12, F.13, A.14, G.15, L.32, E.33, A.34, R.35, G.39, G.40, R.41, T.42, F.54, G.55, G.56, A.57, W.58, E.199, V.227, P.228, V.229, T.257, V.258, P.259, T.262, I.266, K.290, T.331, W.367, F.372, A.376, W.377, A.378, G.402, A.403, A.411, N.412, I.413, D.414, A.416 Ligands: TXU.6 43 PLIP interactions: 43 interactions with chain B Hydrophobic interactions: B:R.41, B:W.367, B:A.376, B:W.377, B:W.377 Hydrogen bonds: B:G.11, B:G.12, B:F.13, B:A.14, B:E.33, B:E.33, B:A.34, B:R.35, B:G.39, B:R.41, B:R.41, B:G.56, B:A.57, B:W.58, B:W.58, B:V.229, B:V.229, B:A.403, B:A.411, B:N.412, B:N.412, B:I.413 Water bridges: B:G.15, B:R.35, B:G.40, B:G.40, B:R.41, B:R.41, B:T.42, B:T.42, B:G.55, B:Q.63, B:D.414 Salt bridges: B:R.41, B:R.41 pi-Stacking: B:F.372, B:W.377, B:W.377

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

PG4.2: 11 residues within 4Å: Chain A: L.85, T.88, P.102, D.103, F.105, G.106, I.109, Y.192, M.196, F.303 Ligands: PG4.3 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.106, A:K.107 PG4.3: 14 residues within 4Å: Chain A: Y.164, L.167, Y.168, M.196, E.199, T.200, F.303, F.305, W.314, W.377, A.411, N.412 Ligands: FDA.1, PG4.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.412

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 11 residues within 4Å: Chain B: L.85, T.88, P.102, D.103, F.105, G.106, I.109, R.110, Y.192, M.196, F.303 No protein-ligand interaction detected (PLIP)

1 x TXU: N-methylmyosmine(Non-covalent)

TXU.6: 11 residues within 4Å: Chain B: W.58, L.167, Y.168, E.199, T.200, W.314, T.331, W.377, A.411, N.412 Ligands: FDA.4 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.167, B:Y.168, B:Y.168, B:T.200, B:W.377, B:W.377, B:A.411 pi-Stacking: B:W.58, B:W.314, B:W.314

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dulchavsky, M. et al., Directed evolution unlocks oxygen reactivity for a nicotine-degrading flavoenzyme. Nat.Chem.Biol. (2023)

Release Date

2023-07-26

Peptides

FAD-dependent oxidoreductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

FAD-dependent oxidoreductase