8OV5

PERIDININ-CHLOROPHYLL-PROTEIN OF AMPHIDINIUM CARTERAE, 100K

PDB DOI: https://doi.org/10.2210/pdb8OV5/pdb

Classification: PHOTOSYNTHESIS
Organism(s): Amphidinium carterae
Expression System: Amphidinium carterae
Mutation(s): No

Deposited: 2023-04-25 Released: 2024-05-15
Deposition Author(s): Hofmann, E., Johanning, S.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.15 Å
R-Value Free: 0.155
R-Value Work: 0.141
R-Value Observed: 0.141

Starting Model: experimental
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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: 124.4 kDa
Atom Count: 11,119
Modelled Residue Count: 936
Deposited Residue Count: 936
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peridinin-chlorophyll a-binding protein 1, chloroplastic	A [auth M], B [auth N], C [auth O]	312	Amphidinium carterae	Mutation(s): 0
UniProt
Find proteins for P80484 (Amphidinium carterae) Explore P80484 Go to UniProtKB: P80484
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P80484
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
W4I (Subject of Investigation/LOI) Query on W4I Download Ideal Coordinates CCD File SDF format, chain J [auth M] SDF format, chain BA [auth N] SDF format, chain JA [auth O] SDF format, chain O [auth M] SDF format, chain OA [auth O] SDF format, chain W [auth N] MOL2 format, chain J [auth M] MOL2 format, chain BA [auth N] MOL2 format, chain JA [auth O] MOL2 format, chain O [auth M] MOL2 format, chain OA [auth O] MOL2 format, chain W [auth N]	BA [auth N] J [auth M] JA [auth O] O [auth M] OA [auth O] BA [auth N], J [auth M], JA [auth O], O [auth M], OA [auth O], W [auth N]	[(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] (5~{Z},8~{Z},11~{Z},14~{Z},17~{Z})-icosa-5,8,11,14,17-pentaenoate C₅₃ H₈₂ O₁₅ NCMDMZMGJSDWGY-ZKVZYNAYSA-N		Interactions Focus chain BA [auth N] Focus chain J [auth M] Focus chain JA [auth O] Focus chain O [auth M] Focus chain OA [auth O] Focus chain W [auth N] Interactions & Density Focus chain BA [auth N] Focus chain J [auth M] Focus chain JA [auth O] Focus chain O [auth M] Focus chain OA [auth O] Focus chain W [auth N]
CLA (Subject of Investigation/LOI) Query on CLA Download Ideal Coordinates CCD File SDF format, chain D [auth M] SDF format, chain DA [auth O] SDF format, chain E [auth M] SDF format, chain Q [auth N] SDF format, chain R [auth N] SDF format, chain EA [auth O] MOL2 format, chain D [auth M] MOL2 format, chain DA [auth O] MOL2 format, chain E [auth M] MOL2 format, chain Q [auth N] MOL2 format, chain R [auth N] MOL2 format, chain EA [auth O]	D [auth M] DA [auth O] E [auth M] EA [auth O] Q [auth N] D [auth M], DA [auth O], E [auth M], EA [auth O], Q [auth N], R [auth N]	CHLOROPHYLL A C₅₅ H₇₂ Mg N₄ O₅ ATNHDLDRLWWWCB-AENOIHSZSA-M		Interactions Focus chain D [auth M] Focus chain DA [auth O] Focus chain E [auth M] Focus chain EA [auth O] Focus chain Q [auth N] Focus chain R [auth N] Interactions & Density Focus chain D [auth M] Focus chain DA [auth O] Focus chain E [auth M] Focus chain EA [auth O] Focus chain Q [auth N] Focus chain R [auth N]
PID (Subject of Investigation/LOI) Query on PID Download Ideal Coordinates CCD File SDF format, chain IA [auth O] SDF format, chain M SDF format, chain X [auth N] SDF format, chain AA [auth N] SDF format, chain F [auth M] SDF format, chain FA [auth O] SDF format, chain G [auth M] SDF format, chain GA [auth O] SDF format, chain H [auth M] SDF format, chain HA [auth O] SDF format, chain I [auth M] SDF format, chain K [auth M] SDF format, chain KA [auth O] SDF format, chain L [auth M] SDF format, chain LA [auth O] SDF format, chain MA [auth O] SDF format, chain N [auth M] SDF format, chain NA [auth O] SDF format, chain S [auth N] SDF format, chain T [auth N] SDF format, chain U [auth N] SDF format, chain V [auth N] SDF format, chain Y [auth N] SDF format, chain Z [auth N] MOL2 format, chain IA [auth O] MOL2 format, chain M MOL2 format, chain X [auth N] MOL2 format, chain AA [auth N] MOL2 format, chain F [auth M] MOL2 format, chain FA [auth O] MOL2 format, chain G [auth M] MOL2 format, chain GA [auth O] MOL2 format, chain H [auth M] MOL2 format, chain HA [auth O] MOL2 format, chain I [auth M] MOL2 format, chain K [auth M] MOL2 format, chain KA [auth O] MOL2 format, chain L [auth M] MOL2 format, chain LA [auth O] MOL2 format, chain MA [auth O] MOL2 format, chain N [auth M] MOL2 format, chain NA [auth O] MOL2 format, chain S [auth N] MOL2 format, chain T [auth N] MOL2 format, chain U [auth N] MOL2 format, chain V [auth N] MOL2 format, chain Y [auth N] MOL2 format, chain Z [auth N]	AA [auth N] F [auth M] FA [auth O] G [auth M] GA [auth O] AA [auth N], F [auth M], FA [auth O], G [auth M], GA [auth O], H [auth M], HA [auth O], I [auth M], IA [auth O], K [auth M], KA [auth O], L [auth M], LA [auth O], M, MA [auth O], N [auth M], NA [auth O], S [auth N], T [auth N], U [auth N], V [auth N], X [auth N], Y [auth N], Z [auth N]	PERIDININ C₃₉ H₅₀ O₇ UYRDHEJRPVSJFM-FROCQLDGSA-N		Interactions Focus chain AA [auth N] Focus chain F [auth M] Focus chain FA [auth O] Focus chain G [auth M] Focus chain GA [auth O] Focus chain H [auth M] Focus chain HA [auth O] Focus chain I [auth M] Focus chain IA [auth O] Focus chain K [auth M] Focus chain KA [auth O] Focus chain L [auth M] Focus chain LA [auth O] Focus chain M Focus chain MA [auth O] Focus chain N [auth M] Focus chain NA [auth O] Focus chain S [auth N] Focus chain T [auth N] Focus chain U [auth N] Focus chain V [auth N] Focus chain X [auth N] Focus chain Y [auth N] Focus chain Z [auth N] Interactions & Density Focus chain AA [auth N] Focus chain F [auth M] Focus chain FA [auth O] Focus chain G [auth M] Focus chain GA [auth O] Focus chain H [auth M] Focus chain HA [auth O] Focus chain I [auth M] Focus chain IA [auth O] Focus chain K [auth M] Focus chain KA [auth O] Focus chain L [auth M] Focus chain LA [auth O] Focus chain M Focus chain MA [auth O] Focus chain N [auth M] Focus chain NA [auth O] Focus chain S [auth N] Focus chain T [auth N] Focus chain U [auth N] Focus chain V [auth N] Focus chain X [auth N] Focus chain Y [auth N] Focus chain Z [auth N]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain CA [auth N] SDF format, chain P [auth M] SDF format, chain PA [auth O] MOL2 format, chain CA [auth N] MOL2 format, chain P [auth M] MOL2 format, chain PA [auth O]	CA [auth N], P [auth M], PA [auth O]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain CA [auth N] Focus chain P [auth M] Focus chain PA [auth O] Interactions & Density Focus chain CA [auth N] Focus chain P [auth M] Focus chain PA [auth O]