SMTL ID : 4tvb.1

Crystal Structure of the Homospermidine Synthase (HSS) from Blastochloris viridis in Complex with NAD, Putrescine and sym-Homospermidine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

homo-dimer

Ligands

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

NAI.1: 35 residues within 4Å: Chain A: I.19, G.20, F.21, G.22, S.23, I.24, G.25, R.26, I.46, D.47, P.48, S.49, A.52, A.67, V.68, T.69, L.93, S.94, V.95, D.96, T.97, T.116, V.117, E.119, G.162, A.163, N.164, P.165, W.231, S.232, E.234, G.235, I.352, V.402 Ligands: 37Z.2 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:I.24, A:W.231, A:V.402 Hydrogen bonds: A:S.23, A:S.23, A:I.24, A:V.68, A:V.68, A:V.95, A:T.116, A:A.163, A:N.164, A:S.232, A:S.232 Water bridges: A:G.22, A:G.22, A:V.117, A:E.119, A:E.119, A:E.234, A:G.235, A:E.239

1 x 37Z: sym-homospermidine(Non-covalent)

37Z.2: 17 residues within 4Å: Chain A: T.116, V.117, A.163, N.164, P.165, E.212, W.231, G.235, E.239, H.298, Y.325, Y.327, D.363, L.365, T.398, V.402 Ligands: NAI.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.231, A:W.231 Hydrogen bonds: A:E.239, A:D.363 Water bridges: A:N.137, A:E.239, A:E.239

1 x 1PS: 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE(Non-covalent)

1PS.3: 6 residues within 4Å: Chain A: S.49, D.50, E.51, D.349, W.350, R.351 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.49, A:D.50, A:E.51 pi-Stacking: A:W.350

1 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.4: 35 residues within 4Å: Chain B: I.19, G.20, F.21, G.22, S.23, I.24, G.25, R.26, I.46, D.47, P.48, S.49, A.52, A.67, V.68, T.69, L.93, S.94, V.95, D.96, T.97, T.116, V.117, E.119, G.162, A.163, N.164, P.165, W.231, S.232, E.234, G.235, I.352, V.402 Ligands: PUT.5 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:W.231, B:V.402 Hydrogen bonds: B:F.21, B:S.23, B:S.23, B:I.24, B:S.49, B:V.68, B:V.68, B:V.95, B:G.162, B:A.163, B:N.164, B:P.165, B:S.232 Water bridges: B:G.22, B:R.26, B:S.49, B:A.52, B:V.117, B:E.119, B:E.119, B:G.235, B:E.239

1 x PUT: 1,4-DIAMINOBUTANE(Non-covalent)

PUT.5: 14 residues within 4Å: Chain B: A.163, N.164, P.165, E.212, W.231, E.239, H.298, Y.325, Y.327, D.363, L.365, T.398, V.402 Ligands: NAD.4 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.231, B:T.398 Hydrogen bonds: B:N.164, B:N.164, B:E.212, B:H.298 Water bridges: B:T.398

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krossa, S. et al., Comprehensive Structural Characterization of the Bacterial Homospermidine Synthase-an Essential Enzyme of the Polyamine Metabolism. Sci Rep (2016)

Release Date

2015-07-08

Peptides

Homospermidine synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Homospermidine synthase

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