SMTL ID : 1kmk.1

E. coli NifS/CsdB protein at 2.20A with the cysteine perselenide intermediate (residue CSZ).

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x SEC: SELENOCYSTEINE(Non-covalent)

SEC.1: 10 residues within 4Å: Chain A: A.30, A.31, H.123, N.175, Q.203, K.226, R.359, C.364, R.379 Ligands: PLP.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.30, A:N.175, A:Q.203, A:R.359, A:R.379, A:R.379 SEC.3: 10 residues within 4Å: Chain B: A.30, A.31, H.123, N.175, Q.203, K.226, R.359, C.364, R.379 Ligands: PLP.4 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.30, B:N.175, B:Q.203, B:R.359, B:R.379, B:R.379

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

PLP.2: 14 residues within 4Å: Chain A: T.94, T.95, H.123, A.125, N.175, D.200, A.202, Q.203, S.223, H.225, K.226 Chain B: G.277, T.278 Ligands: SEC.1 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:H.123, A:K.226 Hydrogen bonds: A:T.95, A:T.95, A:T.95, A:Q.203, A:S.223, A:S.223, B:T.278, B:T.278 Water bridges: A:E.96 Salt bridges: A:H.225, A:K.226 pi-Stacking: A:H.123 PLP.4: 14 residues within 4Å: Chain A: G.277, T.278 Chain B: T.94, T.95, H.123, A.125, N.175, D.200, A.202, Q.203, S.223, H.225, K.226 Ligands: SEC.3 13 PLIP interactions: 1 interactions with chain A, 12 interactions with chain B Hydrogen bonds: A:T.278, B:T.95, B:T.95, B:T.95, B:Q.203, B:S.223, B:S.223 Hydrophobic interactions: B:H.123, B:K.226 Water bridges: B:E.96 Salt bridges: B:H.225, B:K.226 pi-Stacking: B:H.123

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lima, C.D., Analysis of the E. coli NifS CsdB protein at 2.0 A reveals the structural basis for perselenide and persulfide intermediate formation. J.Mol.Biol. (2002)

Release Date

2001-12-21

Peptides

SELENOCYSTEINE LYASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

SELENOCYSTEINE LYASE

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