SMTL ID : 6s49.1

Crystal Structure of the Homospermidine Synthase (HSS) variant E210A from Blastochloris viridis in Complex with NAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

homo-dimer

Ligands

2 x AG2: AGMATINE(Non-covalent)

AG2.1: 11 residues within 4Å: Chain A: R.142, R.149, R.194, S.304, D.307, F.308, A.420, I.422, V.423, D.426, D.427 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:R.142 Water bridges: A:R.149, A:R.149, A:S.304, A:D.307, A:D.307, A:D.307, A:D.307, A:A.420, A:A.420, A:E.424 Salt bridges: A:D.307, A:D.427 AG2.4: 11 residues within 4Å: Chain B: R.142, R.149, R.194, D.307, F.308, A.420, I.422, V.423, E.424, D.426, D.427 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:R.142 Water bridges: B:D.307, B:D.307, B:D.307, B:D.307, B:F.308, B:A.420, B:E.424, B:D.426 Salt bridges: B:D.307, B:D.427

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

SO4.2: 6 residues within 4Å: Chain A: C.267, G.268, R.312, Q.317, A.318, R.321 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.318 Salt bridges: A:R.312, A:R.321 SO4.5: 6 residues within 4Å: Chain B: C.267, G.268, R.312, Q.317, A.318, R.321 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.318 Water bridges: B:G.268 Salt bridges: B:R.312, B:R.321

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

NAD.3: 32 residues within 4Å: Chain A: I.20, G.21, F.22, G.23, S.24, I.25, G.26, R.27, I.47, D.48, P.49, S.50, A.53, A.68, V.69, T.70, L.94, S.95, V.96, D.97, T.98, T.117, V.118, G.163, A.164, N.165, P.166, W.232, S.233, G.236, I.353, V.403 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:I.25, A:W.232, A:V.403 Hydrogen bonds: A:F.22, A:S.24, A:S.24, A:I.25, A:V.69, A:V.69, A:S.95, A:V.96, A:G.163, A:A.164, A:N.165, A:P.166, A:S.233 Water bridges: A:G.26, A:S.50, A:A.53, A:V.118, A:Y.126, A:Y.126 NAD.6: 32 residues within 4Å: Chain B: I.20, G.21, F.22, G.23, S.24, I.25, G.26, I.47, D.48, P.49, S.50, A.53, A.68, V.69, T.70, L.94, S.95, V.96, D.97, T.98, T.117, V.118, E.120, G.163, A.164, N.165, P.166, W.232, S.233, G.236, I.353, V.403 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:I.25, B:W.232, B:V.403 Hydrogen bonds: B:S.24, B:S.24, B:I.25, B:D.48, B:V.69, B:V.69, B:V.96, B:G.163, B:A.164, B:N.165, B:P.166, B:S.233, B:S.233 Water bridges: B:G.23, B:V.118, B:E.120, B:E.120, B:E.240

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Helfrich, F. et al., Structural and catalytic characterization of Blastochloris viridis and Pseudomonas aeruginosa homospermidine synthases supports the essential role of cation-pi interaction. Acta Crystallogr D Struct Biol (2021)

Release Date

2020-07-08

Peptides

Homospermidine synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Homospermidine synthase