SMTL ID : 8cp2.1 (1 other biounit)

Structure of Aspartate-N-hydroxylase (FzmM)from Streptomyces sp. V2: complex with NADPH and L-aspartate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 31 residues within 4Å: Chain A: V.8, G.9, G.11, P.12, R.13, V.40, D.41, P.42, G.48, R.49, V.50, W.51, M.61, N.62, T.63, R.104, A.133, R.134, A.135, A.165, Q.166, G.167, H.168, L.169, N.196, L.503, D.513, A.573, A.574, G.575 Ligands: NAP.2 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:V.50, A:L.503 Hydrogen bonds: A:G.11, A:R.13, A:R.49, A:W.51, A:N.62, A:T.63, A:T.63, A:T.63, A:A.135, A:A.135, A:Q.166, A:H.168, A:H.168, A:G.575 Water bridges: A:G.14, A:V.50, A:V.50, A:R.134, A:V.563, A:V.563 Salt bridges: A:R.13 pi-Stacking: A:W.51 pi-Cation interactions: A:R.134

1 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.2: 19 residues within 4Å: Chain A: L.60, M.61, N.62, R.104, G.215, L.216, G.217, L.218, N.219, D.222, S.257, R.258, R.259, Y.263, I.446, R.502, L.503, A.573 Ligands: FAD.1 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:L.218 Hydrogen bonds: A:L.60, A:R.104, A:L.216, A:L.218, A:N.219, A:S.257, A:R.258, A:R.258, A:R.259, A:Y.263, A:Y.263, A:R.502, A:L.503, A:A.573 Water bridges: A:G.217, A:F.220, A:S.257, A:R.258, A:R.258, A:R.259, A:R.259, A:R.259 Salt bridges: A:R.258 pi-Cation interactions: A:R.258, A:R.258, A:R.502

2 x ASP: ASPARTIC ACID(Non-covalent)

ASP.3: 10 residues within 4Å: Chain A: R.412, N.413, R.416, A.574, G.575, A.576, R.577, S.582, V.583, T.584 11 PLIP interactions: 10 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:N.413, A:R.416, A:G.575, A:R.577, A:V.583, A:T.584, A:T.584, D.3 Water bridges: A:R.577 Salt bridges: A:R.412, A:R.416 ASP.4: 3 residues within 4Å: Chain A: S.79, R.593, R.597 8 PLIP interactions: 4 interactions with chain A, 4 Ligand-Ligand interactions Hydrogen bonds: A:S.79, D.4, D.4 Water bridges: A:R.597, D.4, D.4 Salt bridges: A:R.593, A:R.597

1 x 3NP: 3-NITROPROPANOIC ACID(Non-covalent)

3NP.5: 9 residues within 4Å: Chain A: Y.318, D.354, A.355, R.356, W.357, D.358, R.361, V.362, L.401 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.401 Hydrogen bonds: A:D.354, A:D.358 Salt bridges: A:R.361

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

PEG.6: 4 residues within 4Å: Chain A: W.307, W.359, W.436 Ligands: PEG.7 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.358 PEG.7: 4 residues within 4Å: Chain A: D.431, H.432, W.436 Ligands: PEG.6 No protein-ligand interaction detected (PLIP) PEG.8: 1 residues within 4Å: Chain A: R.258 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.258

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 3 residues within 4Å: Chain A: H.277, V.317, T.320 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.277 Water bridges: A:K.271, A:L.278, A:L.278, A:T.316, A:T.320

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rotilio, L. et al., A biosynthetic aspartate N-hydroxylase performs successive oxidations by holding intermediates at a site away from the catalytic center. J.Biol.Chem. (2023)

Release Date

2023-07-12

Peptides

FAD-binding protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

FAD-binding protein

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