SMTL ID : 5exk.2 (5 other biounits)

Crystal structure of M. tuberculosis lipoyl synthase with 6-thiooctanoyl peptide intermediate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

monomer

Ligands

1 x GLU- SER- THR- XOK- SER- VAL- SER- ASP: Octanoylated peptide from M. tuberculosis H protein(Non-covalent)

GLU-SER-THR-XOK-SER-VAL-SER-ASP.1: 22 residues within 4Å: Chain A: K.45, P.46, P.47, I.49, T.51, Y.59, K.63, V.74, C.75, E.76, A.78, G.79, C.80, P.81, I.83, Q.109, L.270, R.310, S.311, S.312 Ligands: F3S.2, 5AD.4 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:I.49, A:V.74, A:E.76, A:A.78, A:P.81, A:R.310 Hydrogen bonds: A:P.47, A:I.49, A:Y.59, A:K.63, A:K.63, A:A.78, A:G.79, A:Q.109, A:R.310 Water bridges: A:K.45, A:K.45, A:K.45, A:E.76, A:R.271 Salt bridges: A:K.63

1 x F3S: FE3-S4 CLUSTER(Non-covalent)

F3S.2: 9 residues within 4Å: Chain A: C.75, C.80, N.82, I.83, C.86, T.93, R.310, Y.313 Ligands: GLU-SER-THR-XOK-SER-VAL-SER-ASP.1 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.75, A:C.80, A:C.86

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.3: 10 residues within 4Å: Chain A: C.101, R.103, R.104, C.105, F.107, C.108, I.110, R.212, F.215 Ligands: MET.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:C.101, A:C.105, A:C.108, MET.5

1 x 5AD: 5'-DEOXYADENOSINE(Non-covalent)

5AD.4: 14 residues within 4Å: Chain A: V.74, F.107, L.175, N.200, E.202, N.237, I.239, Q.268, Y.269, L.270, P.272, R.310 Ligands: GLU-SER-THR-XOK-SER-VAL-SER-ASP.1, MET.5 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.74 Hydrogen bonds: A:N.200, A:E.202, A:E.202, A:N.237, A:L.270, A:L.270, A:R.310 Water bridges: A:E.202 pi-Stacking: A:F.107

1 x MET: METHIONINE(Non-covalent)

MET.5: 10 residues within 4Å: Chain A: L.95, T.141, G.142, L.175, I.176, P.177, R.212, F.215 Ligands: SF4.3, 5AD.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.144 Water bridges: A:H.199, A:H.199, A:R.212, A:R.212 Salt bridges: A:R.212

1 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.6: 3 residues within 4Å: Chain A: R.161, E.191, S.192 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.161 Hydrogen bonds: A:R.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McLaughlin, M.I. et al., Crystallographic snapshots of sulfur insertion by lipoyl synthase. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-08-10

Peptides

Lipoyl synthase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Lipoyl synthase

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