SMTL ID : 4jye.1

X-ray snapshots of possible intermediates in the time course of synthesis and degradation of protein-bound Fe4S4 clusters.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 9 residues within 4Å: Chain A: C.63, K.65, C.67, Y.69, C.70, R.73, G.109, E.110 Ligands: SAH.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Salt bridges: A:E.110 Metal complexes: A:C.63, A:C.67, A:C.70, SAH.2

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.2: 17 residues within 4Å: Chain A: Y.69, C.70, Q.107, S.108, S.136, G.138, R.159, E.161, R.180, M.199, P.229, F.230, I.231, Y.303, L.305, Y.306 Ligands: SF4.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Q.107 Hydrogen bonds: A:R.159, A:E.161, A:I.231, A:I.231 Water bridges: A:G.138, A:E.161, A:R.180, A:R.180, A:R.180, A:R.180 Salt bridges: A:R.180

5 x 1N7: CHAPSO(Non-covalent)

1N7.3: 5 residues within 4Å: Chain A: V.97, Q.98, F.99, G.100, M.324 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.98, A:F.99 Hydrogen bonds: A:Q.98 Water bridges: A:K.102 1N7.4: 6 residues within 4Å: Chain A: F.36, K.37, D.40, R.284 Ligands: 1N7.5, 1N7.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.36, A:R.284 Hydrogen bonds: A:D.40 Water bridges: A:E.33, A:E.41 1N7.5: 10 residues within 4Å: Chain A: R.29, E.33, F.246, T.247, L.250, V.275, I.281 Ligands: 1N7.4, 1N7.6, CO3.14 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.246, A:L.250, A:V.275, A:I.281, A:I.281 Hydrogen bonds: A:E.33, A:E.33, A:T.247 1N7.6: 3 residues within 4Å: Chain A: R.29 Ligands: 1N7.4, 1N7.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.29, A:R.29 1N7.7: 2 residues within 4Å: Chain A: P.321, E.328 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.321, A:E.328

1 x F3S: FE3-S4 CLUSTER(Non-covalent)

F3S.8: 5 residues within 4Å: Chain A: R.279, C.311, C.319, C.322, V.323 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions, Metal complexes: A:C.311, A:C.311, A:C.319, A:C.322, H2O.1

5 x BR: BROMIDE ION(Non-covalent)(Non-functional Binders)

BR.9: 3 residues within 4Å: Chain A: R.54, T.134, R.155 Ligand excluded by PLIP BR.10: 5 residues within 4Å: Chain A: R.159, T.268, T.269, A.270, Y.306 Ligand excluded by PLIP BR.11: 5 residues within 4Å: Chain A: R.159, G.226, P.266, T.268, M.291 Ligand excluded by PLIP BR.12: 3 residues within 4Å: Chain A: R.64, W.140, P.141 Ligand excluded by PLIP BR.13: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

1 x CO3: CARBONATE ION(Non-functional Binders)

CO3.14: 4 residues within 4Å: Chain A: D.245, F.246, V.275 Ligands: 1N7.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nicolet, Y. et al., X-ray snapshots of possible intermediates in the time course of synthesis and degradation of protein-bound Fe4S4 clusters. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-05-01

Peptides

Biotin synthetase, putative: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Biotin synthetase, putative

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