SMTL ID : 5krq.1

Renalase in complex with NADPH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 42 residues within 4Å: Chain A: I.8, G.9, T.10, G.11, I.12, A.13, G.14, F.31, D.32, K.33, S.34, G.38, G.39, R.40, M.41, M.53, G.54, A.55, Q.56, Y.57, F.58, C.126, R.127, I.128, A.157, T.158, P.159, Q.162, L.166, T.185, A.187, H.232, W.276, A.279, R.280, G.301, D.302, G.307, R.308, V.309, A.312 Ligands: NDP.2 38 PLIP interactions: 38 interactions with chain A Hydrophobic interactions: A:R.40, A:T.185, A:W.276, A:W.276, A:A.279 Hydrogen bonds: A:T.10, A:G.11, A:I.12, A:A.13, A:K.33, A:K.33, A:S.34, A:G.39, A:R.40, A:Q.56, A:Y.57, A:Y.57, A:I.128, A:I.128, A:R.280, A:D.302, A:D.302, A:R.308, A:V.309 Water bridges: A:G.14, A:D.32, A:S.34, A:S.34, A:S.34, A:R.40, A:R.40, A:M.41, A:M.41, A:E.310 Salt bridges: A:R.40, A:R.40 pi-Cation interactions: A:R.280, A:R.280 FAD.3: 42 residues within 4Å: Chain B: I.8, G.9, T.10, G.11, I.12, A.13, G.14, F.31, D.32, K.33, S.34, G.38, G.39, R.40, M.41, M.53, G.54, A.55, Q.56, Y.57, F.58, C.126, R.127, I.128, A.157, T.158, P.159, Q.162, L.166, T.185, A.187, H.232, W.276, A.279, R.280, G.301, D.302, G.307, R.308, V.309, A.312 Ligands: NDP.4 38 PLIP interactions: 38 interactions with chain B Hydrophobic interactions: B:R.40, B:T.185, B:W.276, B:A.279 Hydrogen bonds: B:T.10, B:G.11, B:A.13, B:K.33, B:K.33, B:S.34, B:S.34, B:G.39, B:R.40, B:A.55, B:Q.56, B:Y.57, B:Y.57, B:I.128, B:I.128, B:R.280, B:D.302, B:D.302, B:R.308, B:V.309 Water bridges: B:T.10, B:I.12, B:G.14, B:D.32, B:R.40, B:R.40, B:M.41, B:T.59, B:R.308 Salt bridges: B:R.40, B:R.40 pi-Cation interactions: B:K.33, B:R.280, B:R.280

2 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.2: 14 residues within 4Å: Chain A: Y.57, T.59, R.61, L.85, N.87, S.96, P.97, D.98, Q.100, R.102, F.204, Q.206, R.308 Ligands: FAD.1 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:Y.57, A:T.59, A:S.96, A:D.98, A:R.102, A:Q.206 Water bridges: A:R.61, A:V.205, A:R.308 Salt bridges: A:R.61, A:R.61, A:R.102, A:R.308 pi-Stacking: A:F.204, A:F.204 NDP.4: 14 residues within 4Å: Chain B: Y.57, T.59, R.61, L.85, N.87, S.96, D.98, Q.100, R.102, F.204, Q.206, R.280, R.308 Ligands: FAD.3 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:Y.57, B:T.59, B:S.96, B:D.98, B:D.98, B:R.102, B:Q.206 Water bridges: B:T.59, B:R.61 Salt bridges: B:R.61, B:R.61, B:R.102, B:R.308 pi-Stacking: B:F.204, B:F.204

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Beaupre, B.A. et al., Ligand binding phenomena that pertain to the metabolic function of renalase. Arch.Biochem.Biophys. (2016)

Release Date

2016-11-02

Peptides

Renalase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Renalase

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