SMTL ID : 5d85.1

Staphyloferrin B precursor biosynthetic enzyme SbnA bound to aminoacrylate intermediate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

homo-dimer

Ligands

2 x FLC: CITRATE ANION(Non-covalent)

FLC.1: 13 residues within 4Å: Chain A: S.75, D.98, K.100, G.126, G.127, Y.128, L.129, R.132, R.224, P.227, G.228, A.231, S.232 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:D.98, A:Y.128, A:L.129, A:R.224, A:R.224, A:G.228, A:S.232 Water bridges: A:M.130 Salt bridges: A:K.100, A:R.132, A:R.224, A:R.224 FLC.4: 13 residues within 4Å: Chain B: S.75, D.98, K.100, G.126, G.127, Y.128, L.129, R.132, R.224, P.227, G.228, A.231, S.232 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:D.98, B:Y.128, B:L.129, B:R.224, B:R.224, B:G.228, B:S.232 Water bridges: B:M.130 Salt bridges: B:K.100, B:R.132, B:R.224, B:R.224

2 x P1T: 2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]ACRYLIC ACID(Non-covalent)

P1T.2: 19 residues within 4Å: Chain A: M.46, K.47, T.74, S.75, N.77, L.78, Q.151, Y.152, V.184, S.185, T.186, T.187, G.188, S.189, G.228, S.272, P.298, D.299, Y.304 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:P.298 Hydrogen bonds: A:T.74, A:S.75, A:G.76, A:N.77, A:N.77, A:L.78, A:Q.151, A:S.185, A:T.186, A:T.186, A:T.186, A:T.187, A:G.188, A:S.189, A:S.189, A:S.272 Water bridges: A:S.75, A:Y.152, A:N.157, A:N.157, A:I.190 Salt bridges: A:K.47, A:K.47 P1T.5: 19 residues within 4Å: Chain B: M.46, K.47, T.74, S.75, N.77, L.78, Q.151, Y.152, V.184, S.185, T.186, T.187, G.188, S.189, G.228, S.272, P.298, D.299, Y.304 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:P.298 Hydrogen bonds: B:T.74, B:S.75, B:G.76, B:N.77, B:N.77, B:L.78, B:Q.151, B:S.185, B:T.186, B:T.186, B:T.186, B:T.187, B:G.188, B:S.189, B:S.189, B:S.272 Water bridges: B:S.75, B:Y.152, B:N.157, B:N.157, B:I.190 Salt bridges: B:K.47, B:K.47

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: V.246, I.247, H.248, Q.282 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.248, A:H.248, A:Q.282 GOL.6: 4 residues within 4Å: Chain B: V.246, I.247, H.248, Q.282 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.248, B:H.248, B:Q.282

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

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