SMTL ID : 4xqc.1

Crystal Structure of the Homospermidine Synthase (HSS) from Blastochloris viridis in Complex with NAD and 1,3-diaminopropane.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.27 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 36 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, I.348, V.398 Ligands: 13D.2, 13D.3 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:I.20, A:W.227, A:V.398 Hydrogen bonds: A:S.19, A:S.19, A:I.20, A:D.43, A:S.45, A:V.64, A:V.64, A:V.91, 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:G.231, A:E.235 NAD.8: 34 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 26 PLIP interactions: 26 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:D.43, B:S.45, B:S.45, 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:A.48, B:V.113, B:E.115, B:E.115, B:G.231, B:E.235

2 x 13D: 1,3-DIAMINOPROPANE(Non-covalent)

13D.2: 11 residues within 4Å: Chain A: V.113, A.159, N.160, P.161, W.227, E.235, H.294, Y.321, V.398 Ligands: NAD.1, 13D.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.160, A:E.235 Water bridges: A:N.160, A:E.235, A:E.235 13D.3: 10 residues within 4Å: Chain A: V.91, D.92, V.113, E.115, Y.121, E.230, G.231, S.234 Ligands: NAD.1, 13D.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.91, A:Y.121 Hydrogen bonds: A:D.92, A:E.115, A:Y.121 Water bridges: A:D.92, A:S.234, A:S.234

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

1PS.4: 8 residues within 4Å: Chain A: F.122, L.237, M.336, F.337, G.340, K.341, R.342 Chain B: L.455 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.337 Water bridges: A:R.342 Salt bridges: A:R.342 1PS.9: 8 residues within 4Å: Chain A: L.455 Chain B: F.122, L.237, M.336, F.337, G.340, K.341, R.342 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.237, B:F.337 Water bridges: B:F.122, B:R.342 Salt bridges: B:R.342

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

ACT.5: 3 residues within 4Å: Chain A: E.47, D.345, W.346 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.346 Water bridges: A:W.346 ACT.6: 8 residues within 4Å: Chain A: F.223, V.229, E.230, V.233, M.336, R.342, Q.343, W.346 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.223, A:V.229, A:R.342 Water bridges: A:S.234, A:R.342 Salt bridges: A:R.342 ACT.7: 3 residues within 4Å: Chain A: S.45, D.46, E.47 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.45, A:D.46, A:E.47 Water bridges: A:P.44 ACT.10: 7 residues within 4Å: Chain B: F.223, V.229, E.230, V.233, R.342, Q.343, W.346 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.223, B:V.229, B:R.342 Water bridges: B:S.234, B:R.342, B:W.346 Salt bridges: B:R.342

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