SMTL ID : 4xqe.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 34 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, G.158, A.159, N.160, P.161, W.227, S.228, E.230, G.231, I.348, V.398 Ligands: AG2.5 21 PLIP interactions: 21 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:S.90, A:V.91, A:G.158, A:A.159, A:N.160, A:P.161, A:S.228 Water bridges: A:G.18, A:G.18, A:V.113, A:E.235 NAD.9: 33 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, L.89, S.90, V.91, D.92, T.93, T.112, V.113, G.158, A.159, N.160, P.161, W.227, S.228, E.230, G.231, I.348, V.398 Ligands: AG2.12 23 PLIP interactions: 23 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:S.90, B:V.91, B:G.158, B:A.159, B:N.160, B:P.161, B:S.228, B:S.228 Water bridges: B:G.18, B:G.21, B:D.43, B:S.45, B:V.113

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 6 residues within 4Å: Chain A: C.262, G.263, R.307, Q.312, A.313, R.316 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.313 Water bridges: A:G.263 Salt bridges: A:R.307, A:R.316 SO4.3: 5 residues within 4Å: Chain A: R.213 Chain B: P.217, K.218, P.219, F.220 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:F.220 Water bridges: B:F.220, A:R.213 Salt bridges: A:R.213 SO4.10: 6 residues within 4Å: Chain B: C.262, G.263, R.307, Q.312, A.313, R.316 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.313 Water bridges: B:R.307, B:R.307 Salt bridges: B:R.307, B:R.316 SO4.11: 5 residues within 4Å: Chain A: P.217, K.218, P.219, F.220 Chain B: R.213 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:F.220 Salt bridges: B:R.213

3 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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.45, A:D.46, A:E.47 Water bridges: A:P.44 pi-Stacking: A:W.346 1PS.7: 11 residues within 4Å: Chain A: L.237, P.271, M.336, F.337, G.340, K.341, R.342 Chain B: R.278, R.452, L.455, E.458 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Water bridges: B:R.278, B:R.278, B:Y.288, B:Y.288, A:N.274 Salt bridges: B:R.278, B:R.452 1PS.14: 4 residues within 4Å: Chain B: D.345, W.346, R.347, I.348 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.346 Salt bridges: B:R.347 pi-Stacking: B:W.346

4 x AG2: AGMATINE(Non-covalent)

AG2.5: 16 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 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.227 Hydrogen bonds: A:N.160, A:N.160, A:N.160, A:T.293, A:Y.321 Water bridges: A:S.294 Salt bridges: A:E.235 AG2.6: 10 residues within 4Å: Chain A: R.137, R.144, R.189, S.299, D.302, F.303, I.417, V.418, D.421, D.422 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.137 Water bridges: A:S.299, A:D.302, A:D.302, A:D.302, A:D.302, A:E.419, A:E.419 Salt bridges: A:D.302, A:D.422 AG2.12: 16 residues within 4Å: Chain B: 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.9 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.227 Hydrogen bonds: B:N.160, B:N.160, B:N.160, B:T.293, B:Y.321 Salt bridges: B:E.235 AG2.13: 11 residues within 4Å: Chain B: R.137, R.144, R.189, S.299, D.302, F.303, I.417, V.418, D.421, D.422 Ligands: ACT.15 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:R.137 Water bridges: B:R.144, B:D.302, B:D.302, B:D.302, B:D.302, B:F.303, B:E.419 Salt bridges: B:D.302, B:D.422

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

ACT.8: 2 residues within 4Å: Chain A: W.250, R.469 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.469 ACT.15: 2 residues within 4Å: Chain B: R.189 Ligands: AG2.13 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.190 Water bridges: B:R.189, B:R.189 Salt bridges: B:R.189

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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