4DPB: Plastocyanin A, chloroplastic

The 1.00 Angstrom crystal structure of oxidized (CuII) poplar plastocyanin A at pH 8.0. Determined by X-ray diffraction at 1.0 Å resolution. Released 13 Feb 2013.

Method: X-ray diffraction
Resolution: 1.0 Å
Organism: Populus nigra
Chains: 1
Atoms: 1,117
Mol. weight: 10.56 kDa
Ligands: CU
Released: 13 Feb 2013

Explore 4DPB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4DPB contains 2 α-helices and 10 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain X: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	1
β-strand	14-15	2	1
β-strand	18-21	4	2
β-strand	26-31	6	1
β-strand	37	1	3
β-strand	40-41	2	2
α-helix	52-54	3
β-strand	63	1	3
β-strand	69-73	5	1
β-strand	78-83	6	2
α-helix	85-87	3
β-strand	93-98	6	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Plastocyanin A, chloroplastic	X	protein	99	Populus nigra	P00299 (AlphaFold model)

Sequence of entity 1 (X), FASTA

>4DPB_1 Plastocyanin A, chloroplastic (chains X)
IDVLLGADDGSLAFVPSEFSISPGEKIVFKNNAGFPHNIVFDEDSIPSGVDASKISMSEE
DLLNAKGETFEVALSNKGEYSFYCSPHQGAGMVGKVTVN

Ligands and cofactors

ID	Name	Formula	Copies
CU	Copper (II) ion	Cu	1

Primary citation

Structural comparison of the poplar plastocyanin isoforms PCa and PCb sheds new light on the role of the copper site geometry in interactions with redox partners in oxygenic photosynthesis. Kachalova, G.S., Shosheva, A.C., Bourenkov, G.P. et al. J Inorg Biochem (2012) 115:174-181. DOI 10.1016/j.jinorgbio.2012.07.015 · PubMed

Other PDB entries of the same protein (UniProt P00299 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4DP9 1.0 Å, The 1.00 Angstrom crystal structure of oxidized (CuII) poplar plastocyanin A at pH 6.0
4DPA 1.05 Å, The 1.05 Angstrom crystal structure of reduced (CuI) poplar plastocyanin A at pH 6.0
4DPC 1.06 Å, The 1.06 Angstrom crystal structure of reduced (CuI) poplar plastocyanin A at pH 8.0
4DP8 1.07 Å, The 1.07 Angstrom crystal structure of reduced (CuI) poplar plastocyanin A at pH 4.0
4DP7 1.08 Å, The 1.08 Angstrom crystal structure of oxidized (CuII) poplar plastocyanin A at pH 4.0
1PLC 1.33 Å, Accuracy and precision in protein crystal structure analysis: restrained least-squares…
1JXG 1.6 Å, The 1.6 A Resolution Crystal Structure of a Mutant Poplar Plastocyanin Bearing a 21-25…
1PNC 1.6 Å, Accuracy and precision in protein crystal structure analysis: two independent…
1PND 1.6 Å, Accuracy and precision in protein crystal structure analysis: two independent…
2PCY 1.8 Å, The crystal structure of poplar apoplastocyanin at 1.8-Å resolution. The geometry of the…
5PCY 1.8 Å, Crystal structure analyses of reduced (CUI) poplar plastocyanin at six PH values
3PCY 1.9 Å, The crystal structure of mercury-substituted poplar plastocyanin at 1.9-Å resolution

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