SMTL ID : 1mz4.1

Crystal Structure of Cytochrome c550 from Thermosynechococcus elongatus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

5 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 4 residues within 4Å: Chain A: E.87, I.88, A.89, E.90 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.87, A:A.89, A:E.90 Water bridges: A:I.88 PO4.2: 2 residues within 4Å: Chain A: E.90, V.91 No protein-ligand interaction detected (PLIP) PO4.3: 5 residues within 4Å: Chain A: Y.26, K.30, E.122, L.126 Ligands: PO4.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.26, A:E.122, A:E.122 Salt bridges: A:K.30 PO4.4: 5 residues within 4Å: Chain A: H.118, E.122, L.126, W.130 Ligands: PO4.3 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.43 Salt bridges: A:K.30, A:H.118 PO4.5: 4 residues within 4Å: Chain A: K.24, Q.25, E.28, K.110 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.25 Salt bridges: A:K.110

1 x BCT: BICARBONATE ION(Non-functional Binders)

BCT.6: 5 residues within 4Å: Chain A: N.49, L.52, T.81, Y.82 Ligands: HEC.7 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.49, A:T.81, A:D.83

1 x HEC: HEME C(Covalent)

HEC.7: 26 residues within 4Å: Chain A: A.36, C.37, S.39, C.40, H.41, T.46, T.48, N.49, L.52, D.53, L.54, T.58, L.59, A.62, L.72, Y.75, M.76, Y.82, I.88, H.92, P.93, M.104, I.115, I.119 Ligands: BCT.6, GOL.9 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:T.46, A:L.54, A:L.72, A:Y.75, A:Y.75, A:I.88, A:P.93, A:I.115, A:I.119 Hydrogen bonds: A:N.49 pi-Stacking: A:H.41, A:H.41, A:Y.75, A:H.92 Metal complexes: A:H.41, A:H.92

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 2 residues within 4Å: Chain A: T.56, E.57 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.57 Water bridges: A:D.67 GOL.9: 3 residues within 4Å: Chain A: T.48, N.49 Ligands: HEC.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.49 GOL.10: 7 residues within 4Å: Chain A: P.11, N.13, S.14, G.16, P.65, D.67, N.68 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.14, A:N.68 GOL.11: 2 residues within 4Å: Chain A: R.31, Y.35 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.31 GOL.12: 2 residues within 4Å: Chain A: E.87, R.96 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.87, A:R.96, A:R.96 Water bridges: A:N.78

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kerfeld, C.A. et al., Structural and EPR characterization of the soluble form of cytochrome c-550 and of the psbV2 gene product from the cyanobacterium Thermosynechococcus elongatus. Plant Cell.Physiol. (2003)

Release Date

2003-09-23

Peptides

cytochrome c550: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

cytochrome c550

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