7V3K | pdb_00007v3k

crystal structure of MAJ1

PDB DOI: https://doi.org/10.2210/pdb7V3K/pdb

Classification: LIPID BINDING PROTEIN
Organism(s): Janibacter sp. HTCC2649
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-08-10 Released: 2022-08-17
Deposition Author(s): Wang, Y.H., Cui, R.G.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free:
0.240 (Depositor), 0.238 (DCC)
R-Value Work:
0.187 (Depositor), 0.187 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

crystal structure of MAJ1

Wang, Y.H., Cui, R.G.

To be published.

Macromolecule Content

Total Structure Weight: 135.29 kDa
Atom Count: 9,476
Modeled Residue Count: 1,173
Deposited Residue Count: 1,256
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative lipase	A, B [auth C], C [auth D], D [auth B]	314	Janibacter sp. HTCC2649	Mutation(s): 0 Gene Names: JNB_12713
UniProt
Find proteins for A0ACD6B9J5 (Janibacter sp. HTCC2649) Explore A0ACD6B9J5 Go to UniProtKB: A0ACD6B9J5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6B9J5
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B [auth C] Focus chain C [auth D] Focus chain D [auth B]
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OLA (Subject of Investigation/LOI) Query on OLA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain O [auth D] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain N [auth D] SDF format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain O [auth D] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain N [auth D] MOL2 format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain O [auth D] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain N [auth D] mmCIF format, chain G [auth A]	E [auth A] G [auth A] N [auth D] O [auth D] T [auth B] E [auth A], G [auth A], N [auth D], O [auth D], T [auth B], U [auth B]	OLEIC ACID C₁₈ H₃₄ O₂ ZQPPMHVWECSIRJ-KTKRTIGZSA-N		Interactions Focus chain E [auth A] Focus chain G [auth A] Focus chain N [auth D] Focus chain O [auth D] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth A] Focus chain N [auth D] Focus chain O [auth D] Focus chain T [auth B] Focus chain U [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth C] SDF format, chain P [auth D] SDF format, chain R [auth B] MOL2 format, chain F [auth A] MOL2 format, chain K [auth C] MOL2 format, chain P [auth D] MOL2 format, chain R [auth B] mmCIF format, chain F [auth A] mmCIF format, chain K [auth C] mmCIF format, chain P [auth D] mmCIF format, chain R [auth B]	F [auth A], K [auth C], P [auth D], R [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Focus chain K [auth C] Focus chain P [auth D] Focus chain R [auth B] Interactions & Density Focus chain F [auth A] Focus chain K [auth C] Focus chain P [auth D] Focus chain R [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain L [auth C] SDF format, chain Q [auth D] SDF format, chain S [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain S [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain S [auth B]	H [auth A], I [auth A], L [auth C], Q [auth D], S [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth C] Focus chain Q [auth D] Focus chain S [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth C] Focus chain Q [auth D] Focus chain S [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain V [auth B] SDF format, chain J [auth A] MOL2 format, chain M [auth C] MOL2 format, chain V [auth B] MOL2 format, chain J [auth A] mmCIF format, chain M [auth C] mmCIF format, chain V [auth B] mmCIF format, chain J [auth A]	J [auth A], M [auth C], V [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain M [auth C] Focus chain V [auth B] Interactions & Density Focus chain J [auth A] Focus chain M [auth C] Focus chain V [auth B]