SMTL ID : 5ft5.1

Crystal structure of the cysteine desulfurase CsdA (persulfurated) from Escherichia coli at 2.384 Angstroem resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

homo-dimer

Ligands

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: P.316, A.334, V.400 Ligands: GOL.5 No protein-ligand interaction detected (PLIP) GOL.2: 4 residues within 4Å: Chain A: Y.65, R.69, W.86, W.267 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.69, A:W.86 GOL.3: 4 residues within 4Å: Chain A: A.63, R.64, K.71, E.287 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.71, A:K.71 GOL.4: 4 residues within 4Å: Chain A: H.337, H.338, S.339, T.369 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.338, A:S.339, A:S.339 GOL.5: 3 residues within 4Å: Chain A: P.316, V.400 Ligands: GOL.1 No protein-ligand interaction detected (PLIP) GOL.6: 4 residues within 4Å: Chain A: V.3, F.4, P.6, W.300 No protein-ligand interaction detected (PLIP) GOL.10: 5 residues within 4Å: Chain A: T.28 Chain B: F.42, A.47, T.273, V.276 No protein-ligand interaction detected (PLIP) GOL.11: 5 residues within 4Å: Chain B: Y.65, E.66, A.68, R.69, W.86 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.65, B:Y.65, B:A.68, B:R.69, B:R.69 Water bridges: B:E.66, B:E.70 GOL.12: 3 residues within 4Å: Chain B: R.10, T.381, S.383 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.10 Water bridges: B:S.383, B:D.384 GOL.13: 3 residues within 4Å: Chain B: H.51, R.52, F.55 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.52

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 6 residues within 4Å: Chain A: P.6, R.10, W.300, T.381, K.382, S.383 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.382, A:S.383

2 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.8: 12 residues within 4Å: Chain A: A.26, A.27, H.119, N.171, K.222, R.353, H.357, C.358, R.373 Chain B: K.250, T.273 Ligands: PLP.9 12 PLIP interactions: 3 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:K.250, A:A.27, A:N.171, A:R.353, A:R.353 Water bridges: B:T.273 Salt bridges: B:K.250, A:H.119, A:K.222, A:K.222, A:H.357, A:R.373 TLA.14: 10 residues within 4Å: Chain A: K.250, T.273 Chain B: H.119, N.171, K.222, R.353, H.357, C.358, R.373 Ligands: PLP.15 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:N.171, B:R.373 Water bridges: B:H.357, A:T.273 Salt bridges: B:H.119, B:K.222, B:R.353, B:H.357, B:R.373, A:K.250, A:K.250

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

PLP.9: 15 residues within 4Å: Chain A: G.89, T.90, T.91, H.119, A.121, N.171, D.196, A.198, Q.199, S.219, H.221, K.222 Chain B: G.272, T.273 Ligands: TLA.8 18 PLIP interactions: 3 interactions with chain B, 15 interactions with chain A Hydrogen bonds: B:T.273, B:T.273, A:T.90, A:T.91, A:T.91, A:T.91, A:Q.199, A:S.219, A:S.219, A:K.222 Water bridges: B:K.250, A:E.92 Hydrophobic interactions: A:H.119, A:A.198, A:K.222 Salt bridges: A:H.221, A:K.222 pi-Stacking: A:H.119 PLP.15: 15 residues within 4Å: Chain A: G.272, T.273 Chain B: G.89, T.90, T.91, H.119, A.121, N.171, D.196, A.198, Q.199, S.219, H.221, K.222 Ligands: TLA.14 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:H.119, B:A.198, B:Q.199, B:K.222 Hydrogen bonds: B:T.90, B:T.91, B:T.91, B:Q.199, B:S.219, B:H.221, B:K.222, A:T.273, A:T.273 Water bridges: B:E.92 pi-Stacking: B:H.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fernandez, F.J. et al., Mechanism of Sulfur Transfer Across Protein-Protein Interfaces: The Cysteine Desulfurase Model System. Acs Catalysis (2016)

Release Date

2016-11-23

Peptides

L-CYSTEINE DESULFURASE CSDA: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

L-CYSTEINE DESULFURASE CSDA

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