SMTL ID : 5ft8.1 (3 other biounits)

Crystal structure of the complex between the cysteine desulfurase CsdA and the sulfur-acceptor CsdE in the persulfurated state at 2.50 Angstroem resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-2-2-mer

Ligands

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

PLP.1: 13 residues within 4Å: Chain A: T.92, T.93, H.121, A.123, N.173, D.198, A.200, Q.201, S.221, H.223, K.224 Chain C: G.274, T.275 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:H.121, A:A.200, A:K.224 Hydrogen bonds: A:T.92, A:T.93, A:T.93, A:Q.201, A:S.221, A:S.221, A:K.224, C:T.275, C:T.275 Water bridges: A:T.93 Salt bridges: A:H.223, A:K.224 pi-Stacking: A:H.121 PLP.21: 13 residues within 4Å: Chain A: G.274, T.275 Chain C: T.92, T.93, H.121, A.123, N.173, D.198, A.200, Q.201, S.221, H.223, K.224 16 PLIP interactions: 13 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:H.121, C:A.200, C:K.224 Hydrogen bonds: C:T.92, C:T.93, C:T.93, C:T.93, C:Q.201, C:S.221, C:K.224, A:T.275, A:T.275, A:T.275 Salt bridges: C:H.223, C:K.224 pi-Stacking: C:H.121

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

PEG.2: 8 residues within 4Å: Chain A: Q.101, R.105, P.246, W.247 Chain C: Q.101, R.105, M.130, Q.134 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.105, A:P.246, C:R.105 PEG.3: 6 residues within 4Å: Chain A: R.62, A.65, R.66, A.69, K.73, E.289 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.62, A:R.62, A:K.73 Water bridges: A:R.62, A:E.68 PEG.4: 3 residues within 4Å: Chain A: Q.43, S.46, Q.56 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.46 PEG.17: 6 residues within 4Å: Chain B: S.126, A.127, S.128, R.129, S.130, Q.131 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.126, B:S.130, B:Q.131, B:Q.131 PEG.22: 2 residues within 4Å: Chain C: T.263, S.266 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.266 PEG.23: 4 residues within 4Å: Chain C: K.138, V.139, V.140 Ligands: PEG.24 No protein-ligand interaction detected (PLIP) PEG.24: 3 residues within 4Å: Chain C: E.113, K.138 Ligands: PEG.23 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.113, C:K.138, C:K.138 PEG.25: 3 residues within 4Å: Chain C: Q.76, N.79 Ligands: GOL.29 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.76

26 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 2 residues within 4Å: Chain A: H.189, D.214 Ligand excluded by PLIP GOL.6: 7 residues within 4Å: Chain A: M.3, N.4, V.5, F.6, Q.10, D.293, Y.294 Ligand excluded by PLIP GOL.7: 4 residues within 4Å: Chain A: E.39, Q.43, E.59, R.62 Ligand excluded by PLIP GOL.8: 3 residues within 4Å: Chain A: K.316, R.317, D.395 Ligand excluded by PLIP GOL.9: 5 residues within 4Å: Chain A: N.145, A.146, Q.147, D.151, D.153 Ligand excluded by PLIP GOL.10: 3 residues within 4Å: Chain A: F.44, T.64, V.278 Ligand excluded by PLIP GOL.11: 5 residues within 4Å: Chain A: T.308, E.311, D.312, D.327 Ligands: GOL.12 Ligand excluded by PLIP GOL.12: 4 residues within 4Å: Chain A: E.311, D.312, A.315 Ligands: GOL.11 Ligand excluded by PLIP GOL.13: 4 residues within 4Å: Chain A: A.366, E.367, L.368, G.369 Ligand excluded by PLIP GOL.14: 2 residues within 4Å: Chain A: Q.76, N.79 Ligand excluded by PLIP GOL.15: 1 residues within 4Å: Chain A: D.260 Ligand excluded by PLIP GOL.16: 3 residues within 4Å: Chain A: V.139 Chain C: F.259, D.260 Ligand excluded by PLIP GOL.18: 2 residues within 4Å: Chain B: S.111 Ligands: GOL.20 Ligand excluded by PLIP GOL.19: 2 residues within 4Å: Chain A: E.349 Chain B: W.30 Ligand excluded by PLIP GOL.20: 1 residues within 4Å: Ligands: GOL.18 Ligand excluded by PLIP GOL.26: 2 residues within 4Å: Chain C: E.239, E.242 Ligand excluded by PLIP GOL.27: 4 residues within 4Å: Chain C: A.49, T.64, I.282 Ligands: GOL.28 Ligand excluded by PLIP GOL.28: 4 residues within 4Å: Chain C: Y.67, P.276, V.278 Ligands: GOL.27 Ligand excluded by PLIP GOL.29: 7 residues within 4Å: Chain C: E.72, A.75, Q.76, N.79, A.80, P.81 Ligands: PEG.25 Ligand excluded by PLIP GOL.30: 2 residues within 4Å: Chain C: P.318, G.319 Ligand excluded by PLIP GOL.31: 2 residues within 4Å: Chain C: A.366, G.369 Ligand excluded by PLIP GOL.32: 1 residues within 4Å: Chain C: P.110 Ligand excluded by PLIP GOL.33: 2 residues within 4Å: Chain C: G.369, T.371 Ligand excluded by PLIP GOL.34: 4 residues within 4Å: Chain C: T.308, E.311, D.312, D.327 Ligand excluded by PLIP GOL.35: 3 residues within 4Å: Chain C: Y.67, R.71, W.88 Ligand excluded by PLIP GOL.36: 7 residues within 4Å: Chain D: F.24, A.25, L.27, K.33, E.118, L.119, G.120 Ligand excluded by PLIP

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

Cysteine desulfurase CsdA: AC
Sulfur acceptor protein CsdE: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
Q

D
S

Cysteine desulfurase CsdA

Sulfur acceptor protein CsdE

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