6KXU | pdb_00006kxu

BON1

PDB DOI: https://doi.org/10.2210/pdb6KXU/pdb

Classification: LIPID BINDING PROTEIN
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-09-12 Released: 2020-09-16
Deposition Author(s): Wang, Q.C., Jiang, M.Q., Isupov, M.N., Sun, L.F., Wu, Y.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.83 Å
R-Value Free:
0.249 (Depositor), 0.249 (DCC)
R-Value Work:
0.204 (Depositor), 0.203 (DCC)
R-Value Observed:
0.206 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of an Arabidopsis Copine providing insights into this protein family

Wang, Q.C., Jiang, M.Q., Isupov, M.N., Sun, L.F., Wu, Y.K.

To be published.

Macromolecule Content

Total Structure Weight: 484.16 kDa
Atom Count: 33,483
Modeled Residue Count: 4,290
Deposited Residue Count: 4,367
Unique protein chains: 5

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein BONZAI 1	A, C, D, F	553	Arabidopsis thaliana	Mutation(s): 0 Gene Names: BON1, CPN1, At5g61900, K22G18.2
UniProt
Find proteins for Q941L3 (Arabidopsis thaliana) Explore Q941L3 Go to UniProtKB: Q941L3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q941L3
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein BONZAI 1	B	528	Arabidopsis thaliana	Mutation(s): 0 Gene Names: BON1, CPN1, At5g61900, K22G18.2
UniProt
Find proteins for Q941L3 (Arabidopsis thaliana) Explore Q941L3 Go to UniProtKB: Q941L3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q941L3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein BONZAI 1	E	548	Arabidopsis thaliana	Mutation(s): 0 Gene Names: BON1, CPN1, At5g61900, K22G18.2
UniProt
Find proteins for Q941L3 (Arabidopsis thaliana) Explore Q941L3 Go to UniProtKB: Q941L3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q941L3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein BONZAI 1	G	526	Arabidopsis thaliana	Mutation(s): 0 Gene Names: BON1, CPN1, At5g61900, K22G18.2
UniProt
Find proteins for Q941L3 (Arabidopsis thaliana) Explore Q941L3 Go to UniProtKB: Q941L3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q941L3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein BONZAI 1	H	553	Arabidopsis thaliana	Mutation(s): 0 Gene Names: BON1, CPN1, At5g61900, K22G18.2
UniProt
Find proteins for Q941L3 (Arabidopsis thaliana) Explore Q941L3 Go to UniProtKB: Q941L3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q941L3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain BA [auth F] SDF format, chain EA [auth G] SDF format, chain GA [auth H] SDF format, chain HA [auth H] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain V [auth D] MOL2 format, chain AA [auth F] MOL2 format, chain BA [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain GA [auth H] MOL2 format, chain HA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D] mmCIF format, chain AA [auth F] mmCIF format, chain BA [auth F] mmCIF format, chain EA [auth G] mmCIF format, chain GA [auth H] mmCIF format, chain HA [auth H] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain V [auth D]	AA [auth F] BA [auth F] EA [auth G] GA [auth H] HA [auth H] AA [auth F], BA [auth F], EA [auth G], GA [auth H], HA [auth H], I [auth A], J [auth A], K [auth A], N [auth B], P [auth C], Q [auth C], R [auth C], S [auth C], V [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain BA [auth F] Focus chain EA [auth G] Focus chain GA [auth H] Focus chain HA [auth H] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth D] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth F] Focus chain EA [auth G] Focus chain GA [auth H] Focus chain HA [auth H] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth D]
MN (Subject of Investigation/LOI) Query on MN Download:Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain DA [auth F] SDF format, chain FA [auth G] SDF format, chain IA [auth H] SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain U [auth C] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain Z [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain DA [auth F] MOL2 format, chain FA [auth G] MOL2 format, chain IA [auth H] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain U [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth E] mmCIF format, chain CA [auth F] mmCIF format, chain DA [auth F] mmCIF format, chain FA [auth G] mmCIF format, chain IA [auth H] mmCIF format, chain M [auth A] mmCIF format, chain O [auth B] mmCIF format, chain U [auth C] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth E]	CA [auth F] DA [auth F] FA [auth G] IA [auth H] M [auth A] CA [auth F], DA [auth F], FA [auth G], IA [auth H], M [auth A], O [auth B], U [auth C], X [auth D], Y [auth D], Z [auth E]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain CA [auth F] Focus chain DA [auth F] Focus chain FA [auth G] Focus chain IA [auth H] Focus chain M [auth A] Focus chain O [auth B] Focus chain U [auth C] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth E] Interactions & Density Focus chain CA [auth F] Focus chain DA [auth F] Focus chain FA [auth G] Focus chain IA [auth H] Focus chain M [auth A] Focus chain O [auth B] Focus chain U [auth C] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth E]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain T [auth C] SDF format, chain W [auth D] MOL2 format, chain T [auth C] MOL2 format, chain W [auth D] mmCIF format, chain T [auth C] mmCIF format, chain W [auth D]	T [auth C], W [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain T [auth C] Focus chain W [auth D] Interactions & Density Focus chain T [auth C] Focus chain W [auth D]