SMTL ID : 4zcc.2 (1 other biounit)

Renalase in complex with NADH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 41 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, G.301, D.302, G.307, R.308, V.309, A.312 Ligands: NAI.2 36 PLIP interactions: 36 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: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:K.33 FAD.4: 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: NAI.5 33 PLIP interactions: 33 interactions with chain B Hydrophobic interactions: B:R.40, B:T.185, B:W.276, B:A.279 Hydrogen bonds: B:G.11, B:I.12, B:A.13, B:K.33, B:K.33, B:S.34, B:G.39, B:R.40, B:Q.56, B:Y.57, B:Y.57, B:I.128, B:I.128, B:D.302, B:D.302, B:R.308, B:V.309 Water bridges: B:G.14, B:D.32, B:S.34, B:R.40, B:R.40, B:M.41, B:M.41, B:R.308, B:E.310 Salt bridges: B:R.40, B:R.40 pi-Cation interactions: B:K.33

2 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.2: 17 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, T.185, F.204, A.279, R.280, G.307, R.308 Ligands: FAD.1 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:R.280 Hydrogen bonds: A:T.59, A:S.96, A:D.98, A:R.102, A:A.279, A:R.280 Water bridges: A:Y.57, A:Y.57, A:Q.206, 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 NAI.5: 21 residues within 4Å: Chain B: Y.57, T.59, R.61, L.85, N.87, S.96, D.98, Q.100, R.102, T.185, F.204, D.211, W.212, H.232, A.233, T.234, A.279, R.280, G.307, R.308 Ligands: FAD.4 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:R.280, B:R.280 Hydrogen bonds: B:Y.57, B:T.59, B:S.96, B:D.98, B:D.98, B:R.102, B:T.185, B:A.233, B:R.280 Water bridges: B:R.308 Salt bridges: B:R.61, B:R.61, B:R.102, B:R.308 pi-Stacking: B:F.204, B:F.204 pi-Cation interactions: B:R.280

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

FMT.3: 8 residues within 4Å: Chain A: S.37, G.38, S.42, S.43, K.44, S.110, T.113, R.114 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.37, A:S.43, A:K.44, A:T.113 Water bridges: A:S.37, A:R.117 FMT.6: 7 residues within 4Å: Chain B: S.37, G.38, S.42, S.110, T.113, R.114, R.117 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.37, B:T.113, B:T.113 Water bridges: B:R.117, B:R.117

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hoag, M.R. et al., Bacterial Renalase: Structure and Kinetics of an Enzyme with 2- and 6-Dihydro-beta-NAD(P) Oxidase Activity from Pseudomonas phaseolicola. Biochemistry (2015)

Release Date

2015-07-15

Peptides

Renalase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

Renalase

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