SMTL ID : 6knh.1 (1 other biounit)

Crystal structure of SbnH in complex with citrate, a PLP-dependent decarboxylase in Staphyloferrin B biothesynthesis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

homo-dimer

Ligands

2 x CIT: CITRIC ACID(Non-functional Binders)

CIT.1: 9 residues within 4Å: Chain A: K.50, R.269, R.304, S.308, W.309, Y.373, I.377 Chain B: T.345, K.347 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.373 Hydrogen bonds: A:S.308, A:W.309 Water bridges: A:R.269, A:R.269, A:R.304, A:R.304, A:R.304, B:H.379 Salt bridges: A:K.50, A:R.269, A:R.304, B:K.347, B:K.347 CIT.3: 8 residues within 4Å: Chain A: T.345, K.347 Chain B: R.269, R.304, S.308, W.309, Y.373, I.377 14 PLIP interactions: 5 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:T.345, A:T.345, B:S.308 Water bridges: A:H.379, B:R.269, B:R.269, B:R.304, B:R.304, B:R.304 Salt bridges: A:K.347, A:K.347, B:R.269, B:R.304 Hydrophobic interactions: B:Y.373

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 5 residues within 4Å: Chain A: G.228, C.267, G.268, R.269, Y.373 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.228, A:G.268, A:R.269, A:Y.373 Water bridges: A:H.187, A:H.187, A:N.191, A:I.229, A:I.229, A:E.266 PO4.4: 6 residues within 4Å: Chain B: G.228, E.266, C.267, G.268, R.269, Y.373 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.228, B:G.268, B:R.269, B:Y.373, B:Y.373 Water bridges: B:K.50, B:N.191, B:I.229, B:I.229

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tang, J. et al., Structural Insights into Substrate Recognition and Activity Regulation of the Key Decarboxylase SbnH in Staphyloferrin B Biosynthesis. J.Mol.Biol. (2019)

Release Date

2019-11-13

Peptides

Probable diaminopimelate decarboxylase protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Probable diaminopimelate decarboxylase protein

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