SMTL ID : 4m54.1

The structure of the staphyloferrin B precursor biosynthetic enzyme SbnB bound to N-(1-amino-1-carboxyl-2-ethyl)-glutamic acid and NADH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

homo-dimer

Ligands

2 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.1: 23 residues within 4Å: Chain A: R.63, R.97, R.125, T.126, I.148, G.149, G.151, L.152, I.153, D.175, Q.176, F.177, A.180, C.216, T.217, V.218, T.219, I.238, S.239, P.309, M.310, G.311 Ligands: AE5.3 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:T.126, A:I.153 Hydrogen bonds: A:R.63, A:R.125, A:L.152, A:I.153, A:Q.176, A:Q.176, A:T.217, A:V.218, A:T.219, A:I.238 Water bridges: A:R.97, A:R.97, A:G.151, A:G.151 Salt bridges: A:R.97 NAI.4: 23 residues within 4Å: Chain B: R.63, R.97, R.125, T.126, I.148, G.149, G.151, L.152, I.153, D.175, Q.176, F.177, A.180, C.216, T.217, V.218, T.219, I.238, S.239, P.309, M.310, G.311 Ligands: AE5.6 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:L.152, B:I.153, B:Q.176, B:Q.176, B:T.217, B:V.218, B:T.219, B:I.238 Water bridges: B:R.97, B:R.97, B:G.151, B:G.151, B:T.219, B:T.219 Salt bridges: B:R.97

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 4 residues within 4Å: Chain A: Q.53, D.62, R.63 Chain B: N.110 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: N.110 Chain B: Q.53, D.62, R.63 Ligand excluded by PLIP

2 x AE5: N-[(2S)-2-amino-2-carboxyethyl]-L-glutamic acid(Non-covalent)

AE5.3: 13 residues within 4Å: Chain A: Y.50, R.63, M.67, K.81, I.83, R.97, A.98, S.122, R.125, I.240, M.310, G.311 Ligands: NAI.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.83 Hydrogen bonds: A:Y.50, A:M.310 Salt bridges: A:K.48, A:R.63, A:R.63, A:K.81, A:R.97, A:R.125 AE5.6: 13 residues within 4Å: Chain B: Y.50, R.63, M.67, K.81, I.83, R.97, A.98, S.122, R.125, I.240, M.310, G.311 Ligands: NAI.4 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.83 Hydrogen bonds: B:Y.50, B:Y.50, B:M.310 Salt bridges: B:K.48, B:R.63, 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

2014-07-09

Peptides

Putative ornithine cyclodeaminase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Putative ornithine cyclodeaminase

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