SMTL ID : 5ft4.1

Crystal structure of the cysteine desulfurase CsdA from Escherichia coli at 1.996 Angstroem resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 14 residues within 4Å: Chain A: 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: CIT.4 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:H.119, A:A.198, A:K.222 Hydrogen bonds: A:T.91, A:T.91, A:T.91, A:Q.199, A:S.219, B:T.273, B:T.273 Water bridges: A:E.92 Salt bridges: A:H.221 pi-Stacking: A:H.119 PLP.5: 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: CIT.10 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:H.119, B:A.198, B:K.222 Hydrogen bonds: B:T.90, B:T.91, B:Q.199, B:S.219, B:S.219, B:K.222, A:T.273, A:T.273, A:T.273 Water bridges: B:E.92 Salt bridges: B:H.221 pi-Stacking: B:H.119

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: Y.65, R.69, W.86, W.267 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.69, A:W.86, A:W.267 GOL.3: 7 residues within 4Å: Chain A: Q.99, R.103, P.244, W.245 Chain B: Q.99, R.103, Q.132 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Q.99, A:R.103, A:P.244, B:R.103, B:Q.132 Water bridges: A:W.245, B:Q.99, B:R.103 GOL.6: 2 residues within 4Å: Chain B: Q.263, W.267 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.263 Water bridges: B:Q.263, B:S.264 GOL.7: 2 residues within 4Å: Chain B: P.104, R.105 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.105, B:R.105 GOL.8: 5 residues within 4Å: Chain B: F.42, A.47, T.62, Y.65, V.276 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.62 GOL.9: 5 residues within 4Å: Chain B: Y.65, R.69, W.86, W.267, P.274 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.65, B:R.69 Water bridges: B:R.69

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

CIT.4: 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.1 13 PLIP interactions: 9 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:N.171 Water bridges: A:H.357, B:T.273, B:T.273, B:T.273 Salt bridges: A:H.119, A:K.222, A:K.222, A:R.353, A:H.357, A:R.373, A:R.373, B:K.250 CIT.10: 12 residues within 4Å: Chain A: K.250, T.273 Chain B: A.26, A.27, H.119, N.171, K.222, R.353, H.357, C.358, R.373 Ligands: PLP.5 15 PLIP interactions: 11 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:N.171, B:H.357 Water bridges: B:H.357, B:H.357, A:T.273, A:T.273, A:T.273 Salt bridges: B:H.119, B:K.222, B:K.222, B:R.353, B:H.357, B:R.373, B:R.373, A:K.250 CIT.11: 5 residues within 4Å: Chain B: N.5, P.6, A.7, R.10, W.300 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.5, B:A.7 Salt bridges: B:R.10 CIT.12: 7 residues within 4Å: Chain B: H.337, H.338, S.339, A.354, G.355, G.370, T.371 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:H.338 Hydrogen bonds: B:H.338, B:S.339, B:S.339, B:G.355 Salt bridges: B:H.337, B:H.337, B:H.338, B:H.338

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2016-12-21

Peptides

CYSTEINE DESULFURASE CSDA: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

CYSTEINE DESULFURASE CSDA

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