SMTL ID : 5d86.1

Staphyloferrin B precursor biosynthetic enzyme SbnA Y152F variant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.1: 15 residues within 4Å: Chain A: M.46, K.47, N.77, P.183, V.184, S.185, T.186, T.187, G.188, S.189, G.228, S.272, P.298, D.299, Y.304 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:K.47, A:P.298, A:D.299 Hydrogen bonds: A:N.77, A:P.183, A:S.185, A:T.186, A:T.187, A:G.188, A:S.189, A:S.189, A:S.272 Water bridges: A:N.77, A:N.157, A:N.157, A:S.185, A:I.190 Salt bridges: A:K.47 PLP.5: 15 residues within 4Å: Chain B: M.46, K.47, N.77, P.183, V.184, S.185, T.186, T.187, G.188, S.189, G.228, S.272, P.298, D.299, Y.304 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:K.47, B:P.298, B:D.299 Hydrogen bonds: B:N.77, B:P.183, B:S.185, B:T.186, B:T.187, B:G.188, B:S.189, B:S.189, B:S.272 Water bridges: B:N.77, B:N.157, B:N.157, B:S.185, B:I.190 Salt bridges: B:K.47

4 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain A: A.231, S.232, R.233 No protein-ligand interaction detected (PLIP) MG.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain B: A.231, S.232, R.233 No protein-ligand interaction detected (PLIP)

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.4: 6 residues within 4Å: Chain A: Q.26, D.263, Y.264 Chain B: K.87, I.88, G.90 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.26 Water bridges: A:D.263, B:K.87, B:K.87, B:K.87 TRS.8: 6 residues within 4Å: Chain A: K.87, I.88, G.90 Chain B: Q.26, D.263, Y.264 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Q.26 Water bridges: B:D.263, A:K.87, A:K.87, A:K.87

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kobylarz, M.J. et al., Deciphering the Substrate Specificity of SbnA, the Enzyme Catalyzing the First Step in Staphyloferrin B Biosynthesis. Biochemistry (2016)

Release Date

2016-02-03

Peptides

Probable siderophore biosynthesis protein SbnA: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Probable siderophore biosynthesis protein SbnA