SMTL ID : 4xrg.1

Crystal Structure of the Homospermidine Synthase (HSS) variant H296S from Blastochloris viridis in Complex with NAD, Putrescine and Agmatine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 37 residues within 4Å: Chain A: I.15, G.16, F.17, G.18, S.19, I.20, G.21, R.22, I.42, D.43, P.44, S.45, A.48, A.63, V.64, T.65, L.89, S.90, V.91, D.92, T.93, T.112, V.113, E.115, G.158, A.159, N.160, P.161, W.227, S.228, E.230, G.231, E.235, I.348, V.398 Ligands: AG2.2, PUT.3 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:I.20, A:W.227, A:V.398 Hydrogen bonds: A:S.19, A:S.19, A:S.19, A:I.20, A:S.45, A:V.64, A:V.64, A:V.91, A:T.112, A:G.158, A:A.159, A:N.160, A:P.161, A:S.228, A:S.228 Water bridges: A:G.18, A:G.18, A:V.113, A:E.115, A:E.235 NAD.6: 36 residues within 4Å: Chain B: I.15, G.16, F.17, G.18, S.19, I.20, G.21, R.22, I.42, D.43, P.44, S.45, A.48, A.63, V.64, T.65, L.89, S.90, V.91, D.92, T.93, T.112, V.113, E.115, G.158, A.159, N.160, P.161, W.227, S.228, E.230, G.231, I.348, V.398 Ligands: AG2.7, PUT.8 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:I.20, B:W.227, B:V.398 Hydrogen bonds: B:F.17, B:S.19, B:S.19, B:S.19, B:I.20, B:V.64, B:V.64, B:V.91, B:G.158, B:A.159, B:N.160, B:P.161, B:S.228 Water bridges: B:G.18, B:G.21, B:R.22, B:D.43, B:S.45, B:V.113, B:E.115, B:E.115

2 x AG2: AGMATINE(Non-covalent)

AG2.2: 17 residues within 4Å: Chain A: A.159, N.160, P.161, E.208, W.227, E.235, V.292, T.293, S.294, Y.321, Y.323, D.359, L.361, T.394, V.398 Ligands: NAD.1, PUT.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.227 Hydrogen bonds: A:N.160, A:N.160, A:E.208, A:T.293, A:Y.321 Salt bridges: A:E.235 AG2.7: 18 residues within 4Å: Chain B: A.159, N.160, P.161, E.208, W.227, E.235, V.292, T.293, S.294, E.296, Y.321, Y.323, D.359, L.361, T.394, V.398 Ligands: NAD.6, PUT.8 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.227 Hydrogen bonds: B:N.160, B:N.160, B:T.293, B:S.294, B:Y.321 Salt bridges: B:E.235

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

PUT.3: 16 residues within 4Å: Chain A: A.159, N.160, P.161, E.208, W.227, E.235, S.294, Y.321, Y.323, D.359, L.361, T.394, Q.397, V.398 Ligands: NAD.1, AG2.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.227 Hydrogen bonds: A:N.160, A:N.160, A:Y.321, A:Y.321 PUT.8: 14 residues within 4Å: Chain B: A.159, N.160, P.161, E.208, W.227, E.235, S.294, Y.321, Y.323, L.361, T.394, V.398 Ligands: NAD.6, AG2.7 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.227, B:W.227 Hydrogen bonds: B:N.160, B:N.160 Water bridges: B:Y.323

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

1PS.4: 6 residues within 4Å: Chain A: S.45, D.46, E.47, D.345, W.346, R.347 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.346 Hydrogen bonds: A:D.46, A:E.47 pi-Stacking: A:W.346 1PS.5: 8 residues within 4Å: Chain A: F.122, L.237, M.336, F.337, G.340, K.341, R.342 Chain B: L.455 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.237, A:F.337, B:L.455 Water bridges: A:R.342 Salt bridges: A:R.342

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.9: 9 residues within 4Å: Chain B: K.169, E.185, P.186, T.187, W.192, L.423, D.424, F.425, R.426 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.425 Hydrogen bonds: B:W.192, B:F.425 Water bridges: B:K.169, B:K.169, B:L.423 Salt bridges: B:K.169 ACT.10: 9 residues within 4Å: Chain B: S.165, V.168, K.169, L.172, W.192, I.300, F.303, L.304, D.421 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.168, B:K.169, B:F.303, B:L.304 Hydrogen bonds: B:S.165, B:D.421 Salt bridges: B:K.169

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

2016-01-27

Peptides

Homospermidine synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Homospermidine synthase

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