9KUE | pdb_00009kue

Crystal structure of the soluble green pigment protein from Tettigonia cantans

PDB DOI: https://doi.org/10.2210/pdb9KUE/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Tettigonia cantans
Mutation(s): No

Deposited: 2024-12-03 Released: 2025-04-23
Deposition Author(s): Sluchanko, N.N., Egorkin, N.A., Varfolomeeva, L.A., Popov, V.O., Boyko, K.M.
Funding Organization(s): Ministry of Science and Higher Education of the Russian Federation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free:
0.267 (Depositor), 0.264 (DCC)
R-Value Work:
0.223 (Depositor), 0.228 (DCC)
R-Value Observed:
0.225 (Depositor)

Starting Model: in silico
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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

Crystal structure of the soluble green pigment protein from Tettigonia cantans

Sluchanko, N.N., Egorkin, N.A., Varfolomeeva, L.A., Popov, V.O., Boyko, K.M.

To be published.

Macromolecule Content

Total Structure Weight: 82.87 kDa
Atom Count: 5,823
Modelled Residue Count: 684
Deposited Residue Count: 706
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dibilinoxanthinin (DBXN)	A, D	114	Tettigonia cantans	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Dibilinoxanthinin (DBXN)	B, E	67	Tettigonia cantans	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Dibilinoxanthinin (DBXN)	C, F	172	Tettigonia cantans	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1L6M (Subject of Investigation/LOI) Query on A1L6M Download Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain T [auth F] MOL2 format, chain K [auth C] MOL2 format, chain T [auth F] mmCIF format, chain K [auth C] mmCIF format, chain T [auth F]	K [auth C], T [auth F]	3-[5-[(~{Z})-(3-ethyl-4-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-2-[(~{Z})-[4-(hydroxymethyl)-3-(3-hydroxy-3-oxopropyl)-5-[(~{Z})-[3-methyl-5-oxidanylidene-4-[(1~{S},4~{E},8~{Z})-5,9,13-trimethyl-1-oxidanyl-tetradeca-4,8,12-trienyl]pyrrol-2-ylidene]methyl]pyrrol-2-ylidene]methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid C₄₈ H₆₂ N₄ O₈ XIZXJTXQUCTMIQ-OYUVAKGFSA-N		Interactions Focus chain K [auth C] Focus chain T [auth F] Interactions & Density Focus chain K [auth C] Focus chain T [auth F]
PLC (Subject of Investigation/LOI) Query on PLC Download Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain L [auth C] SDF format, chain O [auth D] SDF format, chain S [auth F] MOL2 format, chain J [auth C] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D] MOL2 format, chain S [auth F] mmCIF format, chain J [auth C] mmCIF format, chain L [auth C] mmCIF format, chain O [auth D] mmCIF format, chain S [auth F]	J [auth C], L [auth C], O [auth D], S [auth F]	DIUNDECYL PHOSPHATIDYL CHOLINE C₃₂ H₆₅ N O₈ P IJFVSSZAOYLHEE-SSEXGKCCSA-O		Interactions Focus chain J [auth C] Focus chain L [auth C] Focus chain O [auth D] Focus chain S [auth F] Interactions & Density Focus chain J [auth C] Focus chain L [auth C] Focus chain O [auth D] Focus chain S [auth F]
LUT (Subject of Investigation/LOI) Query on LUT Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth D] MOL2 format, chain G [auth A] MOL2 format, chain N [auth D] mmCIF format, chain G [auth A] mmCIF format, chain N [auth D]	G [auth A], N [auth D]	(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL C₄₀ H₅₆ O₂ KBPHJBAIARWVSC-NSIPBSJQSA-N		Interactions Focus chain G [auth A] Focus chain N [auth D] Interactions & Density Focus chain G [auth A] Focus chain N [auth D]
AZI Query on AZI Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain M [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth E] SDF format, chain R [auth E] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain R [auth E] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain R [auth E]	H [auth A] I [auth B] M [auth C] P [auth D] Q [auth E] H [auth A], I [auth B], M [auth C], P [auth D], Q [auth E], R [auth E]	AZIDE ION N₃ IVRMZWNICZWHMI-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth E] Interactions & Density Focus chain H [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth E]