SMTL ID : 4mp8.1

Staphyloferrin B precursor biosynthetic enzyme SbnB bound to malonate and NAD+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 24 residues within 4Å: Chain A: R.63, R.97, R.125, T.126, I.148, G.149, C.150, G.151, L.152, I.153, Y.174, D.175, Q.176, F.177, C.216, T.217, V.218, T.219, I.238, S.239, P.309, M.310, G.311 Ligands: MLI.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:T.126, A:I.153 Hydrogen bonds: A:R.63, A:R.125, A:C.150, A:L.152, A:I.153, A:Q.176, A:T.217, A:V.218, A:T.219, A:T.219, A:I.238 Water bridges: A:R.63, A:R.125, A:G.151, A:G.154 Salt bridges: A:R.97, A:R.97 NAD.3: 24 residues within 4Å: Chain B: R.63, R.97, R.125, T.126, I.148, G.149, C.150, G.151, L.152, I.153, Y.174, D.175, Q.176, F.177, C.216, T.217, V.218, T.219, I.238, S.239, P.309, M.310, G.311 Ligands: MLI.4 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:T.126, B:I.153 Hydrogen bonds: B:R.63, B:R.125, B:C.150, B:L.152, B:I.153, B:Q.176, B:T.217, B:V.218, B:T.219, B:I.238 Water bridges: B:R.63, B:R.125, B:G.151, B:G.154, B:T.219 Salt bridges: B:R.97, B:R.97

2 x MLI: MALONATE ION(Non-functional Binders)

MLI.2: 5 residues within 4Å: Chain A: R.63, I.83, R.97, A.98 Ligands: NAD.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.83 Water bridges: A:R.63, A:G.84, A:S.122 Salt bridges: A:R.63, A:R.63, A:K.81, A:R.97 MLI.4: 5 residues within 4Å: Chain B: R.63, I.83, R.97, A.98 Ligands: NAD.3 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.83 Water bridges: B:R.63, B:G.84, B:S.122 Salt bridges: B:R.63, B:R.63, B:K.81, B:R.97

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kobylarz, M.J. et al., Synthesis of L-2,3-diaminopropionic Acid, a siderophore and antibiotic precursor. Chem.Biol. (2014)

Release Date

2014-03-05

Peptides

Putative ornithine cyclodeaminase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Putative ornithine cyclodeaminase

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