SMTL ID : 4r5f.1

X-ray structure of the D199K mutant of the cysteine desulfurase IscS from A. fulgidus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

4 x CA: CALCIUM ION(Non-functional Binders)(Non-covalent)

CA.1: 1 residues within 4Å: Ligands: PG4.5 No protein-ligand interaction detected (PLIP) CA.3: 7 residues within 4Å: Chain A: A.69, N.73, H.98, S.100, D.173, T.175 Ligands: PMP.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.173 CA.15: 1 residues within 4Å: Ligands: PG4.19 No protein-ligand interaction detected (PLIP) CA.17: 7 residues within 4Å: Chain B: A.69, N.73, H.98, S.100, D.173, T.175 Ligands: PMP.18 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.173

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

CL.2: 5 residues within 4Å: Chain A: G.121, K.122, Y.123, G.124, E.125 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain B: G.121, K.122, Y.123, G.124, E.125 Ligand excluded by PLIP

2 x PMP: 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PMP.4: 16 residues within 4Å: Chain A: T.7, S.8, A.69, T.70, N.73, H.98, S.100, N.149, D.173, T.175, A.176, T.194, K.199 Chain B: G.233, S.234 Ligands: CA.3 14 PLIP interactions: 3 interactions with chain B, 11 interactions with chain A Hydrogen bonds: B:S.234, B:S.234, A:T.7, A:A.69, A:T.70, A:T.70, A:N.149, A:K.199 Water bridges: B:Q.226, A:S.67, A:E.71, A:H.98, A:N.149 Hydrophobic interactions: A:T.175 PMP.18: 16 residues within 4Å: Chain A: G.233, S.234 Chain B: T.7, S.8, A.69, T.70, N.73, H.98, S.100, N.149, D.173, T.175, A.176, T.194, K.199 Ligands: CA.17 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:T.175 Hydrogen bonds: B:T.7, B:A.69, B:T.70, B:T.70, B:N.149, B:K.199, A:S.234, A:S.234 Water bridges: B:S.67, B:E.71, B:H.98, B:N.149, A:Q.226

18 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.5: 12 residues within 4Å: Chain A: Y.80, K.87, G.166, K.167, A.168, A.169, D.191, R.212, K.213, E.214, A.215 Ligands: CA.1 Ligand excluded by PLIP PG4.6: 12 residues within 4Å: Chain A: L.55, V.56, N.57, S.177, V.178, G.179, Q.180, I.181, E.182, V.183, D.184, W.254 Ligand excluded by PLIP PG4.7: 6 residues within 4Å: Chain A: N.103, K.106, F.107, K.110 Chain B: L.222 Ligands: PG4.9 Ligand excluded by PLIP PG4.8: 5 residues within 4Å: Chain A: M.99, I.102, K.106, Y.117, H.330 Ligand excluded by PLIP PG4.9: 5 residues within 4Å: Chain A: F.107, K.110, Q.111 Chain B: Q.218 Ligands: PG4.7 Ligand excluded by PLIP PG4.10: 2 residues within 4Å: Chain A: R.295, E.341 Ligand excluded by PLIP PG4.11: 2 residues within 4Å: Chain A: Y.298, R.374 Ligand excluded by PLIP PG4.12: 7 residues within 4Å: Chain A: R.15, E.18, A.19, K.245, E.248, I.249, M.252 Ligand excluded by PLIP PG4.13: 7 residues within 4Å: Chain A: A.2, Y.3, P.11, Y.353 Chain B: T.25, F.28, Y.37 Ligand excluded by PLIP PG4.19: 12 residues within 4Å: Chain B: Y.80, K.87, G.166, K.167, A.168, A.169, D.191, R.212, K.213, E.214, A.215 Ligands: CA.15 Ligand excluded by PLIP PG4.20: 12 residues within 4Å: Chain B: L.55, V.56, N.57, S.177, V.178, G.179, Q.180, I.181, E.182, V.183, D.184, W.254 Ligand excluded by PLIP PG4.21: 6 residues within 4Å: Chain A: L.222 Chain B: N.103, K.106, F.107, K.110 Ligands: PG4.23 Ligand excluded by PLIP PG4.22: 5 residues within 4Å: Chain B: M.99, I.102, K.106, Y.117, H.330 Ligand excluded by PLIP PG4.23: 5 residues within 4Å: Chain A: Q.218 Chain B: F.107, K.110, Q.111 Ligands: PG4.21 Ligand excluded by PLIP PG4.24: 2 residues within 4Å: Chain B: R.295, E.341 Ligand excluded by PLIP PG4.25: 2 residues within 4Å: Chain B: Y.298, R.374 Ligand excluded by PLIP PG4.26: 7 residues within 4Å: Chain B: R.15, E.18, A.19, K.245, E.248, I.249, M.252 Ligand excluded by PLIP PG4.27: 7 residues within 4Å: Chain A: T.25, F.28, Y.37 Chain B: A.2, Y.3, P.11, Y.353 Ligand excluded by PLIP

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.14: 5 residues within 4Å: Chain A: Q.327, P.328, S.329, H.330, V.331 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.330 Salt bridges: A:H.330 ACT.28: 5 residues within 4Å: Chain B: Q.327, P.328, S.329, H.330, V.331 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.330 Salt bridges: B:H.330

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pagnier, A. et al., IscS from Archaeoglobus fulgidus has no desulfurase activity but may provide a cysteine ligand for [Fe2S2] cluster assembly. Biochim.Biophys.Acta (2015)

Release Date

2014-12-17

Peptides

Cysteine desulfurase IscS 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Cysteine desulfurase IscS 2