SMTL ID : 4mpd.1

Staphyloferrin B precursor biosynthetic enzyme SbnB bound a-ketoglutarate and NAD+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x NAJ: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM)(Non-covalent)

NAJ.1: 22 residues within 4Å: Chain A: R.63, R.97, S.122, R.125, T.126, G.149, G.151, L.152, I.153, D.175, Q.176, F.177, C.216, T.217, V.218, T.219, Y.223, I.238, P.309, M.310, G.311 Ligands: AKG.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:T.126, A:I.153 Hydrogen bonds: A:R.63, A:R.125, A:G.151, A:L.152, A:I.153, A:Q.176, A:F.177, A:T.217, A:V.218, A:I.238 Salt bridges: A:R.97, A:R.97 NAJ.3: 22 residues within 4Å: Chain B: R.63, R.97, S.122, R.125, T.126, G.149, G.151, L.152, I.153, D.175, Q.176, F.177, C.216, T.217, V.218, T.219, Y.223, I.238, P.309, M.310, G.311 Ligands: AKG.4 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:T.126, B:I.153 Hydrogen bonds: B:R.63, B:R.125, B:G.151, B:L.152, B:I.153, B:Q.176, B:F.177, B:T.217, B:V.218, B:I.238 Salt bridges: B:R.97, B:R.97

2 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.2: 13 residues within 4Å: Chain A: K.48, R.63, I.65, M.67, K.81, I.83, S.85, R.97, A.98, R.125, M.310, G.311 Ligands: NAJ.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.83 Hydrogen bonds: A:K.81, A:R.125 Salt bridges: A:K.48, A:R.63, A:K.81, A:R.97, A:R.125 AKG.4: 13 residues within 4Å: Chain B: K.48, R.63, I.65, M.67, K.81, I.83, S.85, R.97, A.98, R.125, M.310, G.311 Ligands: NAJ.3 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.83 Hydrogen bonds: B:K.81, B:R.125 Salt bridges: B:K.48, B:R.63, B:K.81, B:R.97, B:R.125

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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