8OW6

PERIDININ-CHLOROPHYLL-PROTEIN OF HETEROCAPSA PYGMAEA, 100K

PDB DOI: https://doi.org/10.2210/pdb8OW6/pdb

Classification: PHOTOSYNTHESIS
Organism(s): Heterocapsa pygmaea
Mutation(s): No

Deposited: 2023-04-27 Released: 2024-05-15
Deposition Author(s): Hofmann, E., Schulte, T.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.171
R-Value Work: 0.149
R-Value Observed: 0.163

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structural and Spectroscopic Characterization of the Peridinin-Chlorophyll a-Protein (PCP) Complex from Heterocapsa pygmaea (HPPCP)

Schulte, T., Magdaong, N.C.M., Di Valentin, M., Agostini, A., Tait, C.E., Niedzwiedzki, D.M., Carbonera, D., Hofmann, E.

To be published.

Macromolecule Content

Total Structure Weight: 80.37 kDa
Atom Count: 6,601
Modelled Residue Count: 596
Deposited Residue Count: 596
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peridinin-chl a protein	A, C	149	Heterocapsa pygmaea	Mutation(s): 0
UniProt
Find proteins for Q9FEY4 (Heterocapsa pygmaea) Explore Q9FEY4 Go to UniProtKB: Q9FEY4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9FEY4
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peridinin-chl a protein	B, D	149	Heterocapsa pygmaea	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
W4O (Subject of Investigation/LOI) Query on W4O Download Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain J [auth A] SDF format, chain R [auth B] SDF format, chain Z [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain R [auth B] MOL2 format, chain Z [auth C]	FA [auth D], J [auth A], R [auth B], Z [auth C]	[(2~{S})-3-[(2~{R},3~{R},4~{S},5~{R},6~{R})-6-[[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2-[(6~{Z},9~{Z},12~{Z},15~{Z})-octadeca-6,9,12,15-tetraenoyl]oxy-propyl] (6~{Z},9~{Z},12~{Z},15~{Z})-octadeca-6,9,12,15-tetraenoate C₅₁ H₈₀ O₁₅ VXOQBABFAYTJKD-LAAVQGTGSA-N		Interactions Focus chain FA [auth D] Focus chain J [auth A] Focus chain R [auth B] Focus chain Z [auth C] Interactions & Density Focus chain FA [auth D] Focus chain J [auth A] Focus chain R [auth B] Focus chain Z [auth C]
CLA (Subject of Investigation/LOI) Query on CLA Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain E [auth A] SDF format, chain M [auth B] SDF format, chain U [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain U [auth C]	AA [auth D], E [auth A], M [auth B], U [auth C]	CHLOROPHYLL A C₅₅ H₇₂ Mg N₄ O₅ ATNHDLDRLWWWCB-AENOIHSZSA-M		Interactions Focus chain AA [auth D] Focus chain E [auth A] Focus chain M [auth B] Focus chain U [auth C] Interactions & Density Focus chain AA [auth D] Focus chain E [auth A] Focus chain M [auth B] Focus chain U [auth C]
PID (Subject of Investigation/LOI) Query on PID Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C]	BA [auth D] CA [auth D] DA [auth D] EA [auth D] F [auth A] BA [auth D], CA [auth D], DA [auth D], EA [auth D], F [auth A], G [auth A], H [auth A], I [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], V [auth C], W [auth C], X [auth C], Y [auth C]	PERIDININ C₃₉ H₅₀ O₇ UYRDHEJRPVSJFM-FROCQLDGSA-N		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A]	L [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
K Query on K Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain S [auth B] MOL2 format, chain K [auth A] MOL2 format, chain S [auth B]	K [auth A], S [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain S [auth B] Interactions & Density Focus chain K [auth A] Focus chain S [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain T [auth B] MOL2 format, chain T [auth B]	T [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain T [auth B] Interactions & Density Focus chain T [auth B]