5V85 | pdb_00005v85

The crystal structure of the protein of DegV family COG1307 from Ruminococcus gnavus ATCC 29149 (alternative refinement of PDB 3JR7 with Vaccenic acid)

PDB DOI: https://doi.org/10.2210/pdb5V85/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Mediterraneibacter gnavus ATCC 29149
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2017-03-21 Released: 2018-11-21
Deposition Author(s): Cuypers, M.G., Ericson, M., subramanian, C., White, S.W., Rock, C.O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.198 (Depositor), 0.196 (DCC)
R-Value Work:
0.169 (Depositor), 0.169 (DCC)
R-Value Observed:
0.170 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 3JR7

Literature

The crystal structure of the Staphylococcus aureus Fatty acid Kinase (Fak) B1 protein loaded with palmitic acid to 1.83 Angstroem resolution

Cuypers, M.G., Ericson, M., Subramanian, C., Broussard, T.C., Miller, D.J., White, S.W., Rock, C.O.

(2018) J Biological Chem

Macromolecule Content

Total Structure Weight: 68.26 kDa
Atom Count: 5,055
Modeled Residue Count: 557
Deposited Residue Count: 596
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EDD domain protein, DegV family	A, B	298	Mediterraneibacter gnavus ATCC 29149	Mutation(s): 0 Gene Names: RUMGNA_03254
UniProt
Find proteins for A7B6P0 (Mediterraneibacter gnavus (strain ATCC 29149 / DSM 114966 / JCM 6515 / VPI C7-9)) Explore A7B6P0 Go to UniProtKB: A7B6P0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A7B6P0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VCA Query on VCA Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain C [auth A]	C [auth A], H [auth B]	VACCENIC ACID C₁₈ H₃₄ O₂ UWHZIFQPPBDJPM-FPLPWBNLSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth A], I [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A], J [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain G [auth A] Focus chain J [auth B]