SMTL ID : 7us3.1

Structure of Putrescine N-hydroxylase Involved Complexed with NADP+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 28 residues within 4Å: Chain A: G.33, V.34, G.35, P.36, F.37, F.56, D.57, S.58, K.59, W.64, H.65, I.68, L.75, Q.76, I.77, S.139, F.140, V.141, G.174, T.175, G.176, T.177, Y.357, N.398, P.409, D.410, L.411 Ligands: NAP.2 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:H.65, A:I.68, A:Y.357 Hydrogen bonds: A:G.33, A:V.34, A:G.35, A:F.37, A:S.58, A:K.59, A:W.64, A:Q.76, A:V.141, A:V.141, A:T.177, A:N.398, A:P.409, A:P.409, A:L.411 Water bridges: A:N.38, A:G.176, A:G.176 FAD.5: 28 residues within 4Å: Chain B: G.33, V.34, G.35, P.36, F.37, F.56, D.57, S.58, K.59, W.64, H.65, I.68, L.75, Q.76, I.77, S.139, F.140, V.141, G.174, T.175, G.176, T.177, Y.357, N.398, P.409, D.410, L.411 Ligands: NAP.4 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:H.65, B:I.68, B:Y.357 Hydrogen bonds: B:G.33, B:V.34, B:G.35, B:F.37, B:S.58, B:K.59, B:W.64, B:Q.76, B:V.141, B:V.141, B:T.177, B:N.398, B:P.409, B:P.409, B:L.411 Water bridges: B:N.38, B:G.176, B:G.176, B:T.177 Salt bridges: B:H.65 FAD.8: 28 residues within 4Å: Chain C: G.33, V.34, G.35, P.36, F.37, F.56, D.57, S.58, K.59, W.64, H.65, I.68, L.75, Q.76, I.77, S.139, F.140, V.141, G.174, T.175, G.176, T.177, Y.357, N.398, P.409, D.410, L.411 Ligands: NAP.7 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:H.65, C:I.68, C:Y.357 Hydrogen bonds: C:V.34, C:G.35, C:F.37, C:S.58, C:W.64, C:Q.76, C:V.141, C:V.141, C:T.177, C:N.398, C:P.409, C:P.409, C:L.411 Water bridges: C:N.38, C:K.59, C:D.63, C:G.176, C:G.176, C:T.177 FAD.11: 28 residues within 4Å: Chain D: G.33, V.34, G.35, P.36, F.37, F.56, D.57, S.58, K.59, W.64, H.65, I.68, L.75, Q.76, I.77, S.139, F.140, V.141, G.174, T.175, G.176, T.177, Y.357, N.398, P.409, D.410, L.411 Ligands: NAP.10 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:H.65, D:I.68, D:Y.357 Hydrogen bonds: D:G.33, D:V.34, D:F.37, D:S.58, D:W.64, D:Q.76, D:V.141, D:V.141, D:T.177, D:N.398, D:P.409, D:P.409, D:L.411 Water bridges: D:V.34, D:G.35, D:K.59, D:G.176, D:G.176, D:T.177

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

NAP.2: 24 residues within 4Å: Chain A: T.74, L.75, Q.76, R.118, V.214, G.215, G.216, G.217, Q.218, S.219, E.222, T.242, K.243, N.284, Y.287, K.288, C.319, A.320, L.321, A.354, L.355, G.356, Y.357 Ligands: FAD.1 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:Q.218 Hydrogen bonds: A:T.74, A:Q.76, A:R.118, A:G.216, A:G.217, A:Q.218, A:S.219, A:S.219, A:T.242, A:K.243, A:Y.287, A:L.321, A:L.321, A:G.356 Water bridges: A:S.195, A:Q.218, A:Q.218, A:G.220, A:G.220, A:N.284, A:G.289, A:A.354, A:Y.357 Salt bridges: A:K.243, A:K.288 pi-Cation interactions: A:K.243 NAP.4: 24 residues within 4Å: Chain B: T.74, L.75, Q.76, R.118, V.214, G.215, G.216, G.217, Q.218, S.219, E.222, T.242, K.243, N.284, Y.287, K.288, C.319, A.320, L.321, A.354, L.355, G.356, Y.357 Ligands: FAD.5 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:Q.218 Hydrogen bonds: B:T.74, B:Q.76, B:Q.76, B:R.118, B:G.216, B:G.217, B:Q.218, B:S.219, B:S.219, B:K.243, B:N.284, B:Y.287, B:L.321, B:L.321 Water bridges: B:Q.218, B:Q.218, B:G.220, B:G.289, B:G.356, B:G.356, B:Y.357 Salt bridges: B:K.243, B:K.288 pi-Cation interactions: B:K.243 NAP.7: 25 residues within 4Å: Chain C: T.74, L.75, Q.76, R.118, V.214, G.215, G.216, G.217, Q.218, S.219, E.222, T.242, K.243, A.244, N.284, Y.287, K.288, C.319, A.320, L.321, A.354, L.355, G.356, Y.357 Ligands: FAD.8 29 PLIP interactions: 29 interactions with chain C Hydrophobic interactions: C:Q.218, C:Q.218 Hydrogen bonds: C:T.74, C:Q.76, C:R.118, C:G.216, C:G.217, C:Q.218, C:S.219, C:S.219, C:T.242, C:K.243, C:Y.287, C:L.321, C:L.321 Water bridges: C:T.74, C:S.195, C:S.195, C:G.216, C:Q.218, C:G.220, C:G.220, C:T.242, C:G.289, C:G.289, C:Y.357 Salt bridges: C:K.243, C:K.288 pi-Cation interactions: C:K.243 NAP.10: 24 residues within 4Å: Chain D: T.74, L.75, Q.76, R.118, V.214, G.215, G.216, G.217, Q.218, S.219, E.222, T.242, K.243, N.284, Y.287, K.288, C.319, A.320, L.321, A.354, L.355, G.356, Y.357 Ligands: FAD.11 32 PLIP interactions: 32 interactions with chain D Hydrophobic interactions: D:Q.218 Hydrogen bonds: D:T.74, D:Q.76, D:Q.76, D:R.118, D:G.216, D:G.217, D:Q.218, D:S.219, D:S.219, D:T.242, D:K.243, D:Y.287, D:L.321, D:L.321, D:G.356 Water bridges: D:S.195, D:S.195, D:G.216, D:Q.218, D:Q.218, D:G.220, D:T.242, D:N.284, D:N.284, D:K.288, D:G.289, D:Y.357 Salt bridges: D:K.243, D:K.288, D:K.288 pi-Cation interactions: D:K.243

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

PGE.3: 5 residues within 4Å: Chain A: E.190, Q.191, K.208, N.329, E.349 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.208 PGE.9: 5 residues within 4Å: Chain D: E.190, D.204, K.208, N.329, E.349 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.208

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

PG4.6: 3 residues within 4Å: Chain C: D.60, K.138, P.160 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.60, C:K.138

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lyons, N.S. et al., Kinetic and Structural Characterization of a Flavin-Dependent Putrescine N -Hydroxylase from Acinetobacter baumannii. Biochemistry (2022)

Release Date

2022-11-30

Peptides

Putrescine N-hydroxylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Putrescine N-hydroxylase