SMTL ID : 4hvk.1

Crystal structure and functional studies of an unusual L-cysteine desulfurase from Archaeoglobus fulgidus.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.43 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: 6 residues within 4Å: Chain A: 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: 6 residues within 4Å: Chain B: 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: 12 residues within 4Å: Chain A: T.7, A.69, T.70, N.73, H.98, S.100, N.149, D.173, T.175 Chain B: G.233, S.234 Ligands: CA.3 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:T.175 Hydrogen bonds: A:T.7, A:A.69, A:T.70, A:T.70, A:N.149, B:S.234, B:S.234 Water bridges: A:E.71, A:N.149, A:S.196, A:S.196, B:Q.226 PMP.18: 12 residues within 4Å: Chain A: G.233, S.234 Chain B: T.7, A.69, T.70, N.73, H.98, S.100, N.149, D.173, T.175 Ligands: CA.17 13 PLIP interactions: 10 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:N.149, B:T.175, A:S.234, A:S.234 Water bridges: B:E.71, B:N.149, B:S.196, B:S.196, A:Q.226

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

PG4.5: 10 residues within 4Å: Chain A: Y.80, G.166, K.167, A.168, A.169, D.191, R.212, K.213, E.214 Ligands: CA.1 Ligand excluded by PLIP PG4.6: 8 residues within 4Å: Chain A: L.55, S.177, V.178, G.179, I.181, E.182, V.183, W.254 Ligand excluded by PLIP PG4.7: 6 residues within 4Å: Chain A: P.22, Y.23, E.26, S.27, Y.37, K.40 Ligand excluded by PLIP PG4.8: 6 residues within 4Å: Chain A: N.103, K.106, F.107, K.110 Chain B: L.222 Ligands: PG4.10 Ligand excluded by PLIP PG4.9: 3 residues within 4Å: Chain A: I.102, K.106, Y.117 Ligand excluded by PLIP PG4.10: 3 residues within 4Å: Chain A: K.110 Chain B: Q.218 Ligands: PG4.8 Ligand excluded by PLIP PG4.11: 3 residues within 4Å: Chain A: Y.279, R.295, E.341 Ligand excluded by PLIP PG4.12: 2 residues within 4Å: Chain A: Y.298, R.374 Ligand excluded by PLIP PG4.13: 6 residues within 4Å: Chain A: R.15, E.18, A.19, K.245, E.248, M.252 Ligand excluded by PLIP PG4.14: 2 residues within 4Å: Chain A: Y.353 Chain B: F.28 Ligand excluded by PLIP PG4.19: 10 residues within 4Å: Chain B: Y.80, G.166, K.167, A.168, A.169, D.191, R.212, K.213, E.214 Ligands: CA.15 Ligand excluded by PLIP PG4.20: 8 residues within 4Å: Chain B: L.55, S.177, V.178, G.179, I.181, E.182, V.183, W.254 Ligand excluded by PLIP PG4.21: 6 residues within 4Å: Chain B: P.22, Y.23, E.26, S.27, Y.37, K.40 Ligand excluded by PLIP PG4.22: 6 residues within 4Å: Chain A: L.222 Chain B: N.103, K.106, F.107, K.110 Ligands: PG4.24 Ligand excluded by PLIP PG4.23: 3 residues within 4Å: Chain B: I.102, K.106, Y.117 Ligand excluded by PLIP PG4.24: 3 residues within 4Å: Chain A: Q.218 Chain B: K.110 Ligands: PG4.22 Ligand excluded by PLIP PG4.25: 3 residues within 4Å: Chain B: Y.279, R.295, E.341 Ligand excluded by PLIP PG4.26: 2 residues within 4Å: Chain B: Y.298, R.374 Ligand excluded by PLIP PG4.27: 6 residues within 4Å: Chain B: R.15, E.18, A.19, K.245, E.248, M.252 Ligand excluded by PLIP PG4.28: 2 residues within 4Å: Chain A: F.28 Chain B: Y.353 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamanaka, Y. et al., Crystal structure and functional studies of an unusual L-cysteine desulfurase from Archaeoglobus fulgidus. Dalton Trans (2013)

Release Date

2012-12-05

Peptides

Probable cysteine desulfurase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Probable cysteine desulfurase 2

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