8JUR | pdb_00008jur

Crystal structure of Chitoporin from Vibrio harveyi in complex with gentamicin c1a (multiple binding sites)

PDB DOI: https://doi.org/10.2210/pdb8JUR/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Vibrio harveyi
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD

Deposited: 2023-06-27 Released: 2024-07-03
Deposition Author(s): Sanram, S., Suginta, W., Robinson, R.
Funding Organization(s): Vidyasirimedhi Institute of Science and Technology (VISTEC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.92 Å
R-Value Free:
0.266 (Depositor), 0.267 (DCC)
R-Value Work:
0.203 (Depositor), 0.207 (DCC)
R-Value Observed:
0.206 (Depositor)

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

Crystal structure of Chitoporin from Vibrio harveyi in complex with gentamicin c1a (multiple binding sites)

Sanram, S., Suginta, W.

To be published.

Macromolecule Content

Total Structure Weight: 117.16 kDa
Atom Count: 8,198
Modeled Residue Count: 1,050
Deposited Residue Count: 1,050
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitoporin	A, B, C	350	Vibrio harveyi	Mutation(s): 0 Gene Names: chiP, AL538_13355, VCHENC02_0932 Membrane Entity: Yes
UniProt
Find proteins for L0RVU0 (Vibrio harveyi) Explore L0RVU0 Go to UniProtKB: L0RVU0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	L0RVU0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LLL Query on LLL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	(2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL C₁₉ H₃₉ N₅ O₇ VEGXETMJINRLTH-BOZYPMBZSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
C8E (Subject of Investigation/LOI) Query on C8E Download:Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain I [auth B] SDF format, chain D [auth A] MOL2 format, chain M [auth C] MOL2 format, chain I [auth B] MOL2 format, chain D [auth A] mmCIF format, chain M [auth C] mmCIF format, chain I [auth B] mmCIF format, chain D [auth A]	D [auth A], I [auth B], M [auth C]	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE C₁₆ H₃₄ O₅ FEOZZFHAVXYAMB-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Focus chain M [auth C] Interactions & Density Focus chain D [auth A] Focus chain I [auth B] Focus chain M [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] J [auth B] K [auth B] E [auth A], F [auth A], G [auth A], J [auth B], K [auth B], L [auth B], N [auth C], O [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C]