8JUQ | pdb_00008juq

Crystal structure of Chitoporin from Vibrio harveyi in complex with gentamicin c1a

PDB DOI: https://doi.org/10.2210/pdb8JUQ/pdb

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

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: 2.21 Å
R-Value Free:
0.222 (Depositor), 0.220 (DCC)
R-Value Work:
0.189 (Depositor), 0.190 (DCC)
R-Value Observed:
0.191 (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

Sanram, S., Suginta, W.

To be published.

Macromolecule Content

Total Structure Weight: 235.45 kDa
Atom Count: 17,092
Modeled Residue Count: 2,100
Deposited Residue Count: 2,100
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitoporin	A B C D [auth G] E [auth H] A, B, C, D [auth G], E [auth H], F [auth I]	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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 Q [auth C] MOL2 format, chain Q [auth C] mmCIF format, chain Q [auth C]	Q [auth C]	(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 Q [auth C] Interactions & Density Focus chain Q [auth C]
C8E (Subject of Investigation/LOI) Query on C8E Download Ideal Coordinates CCD File SDF format, chain CA [auth G] SDF format, chain GA [auth H] SDF format, chain J [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain U [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain K [auth A] MOL2 format, chain CA [auth G] MOL2 format, chain GA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain U [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain K [auth A] mmCIF format, chain CA [auth G] mmCIF format, chain GA [auth H] mmCIF format, chain J [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain U [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain K [auth A]	CA [auth G] GA [auth H] J [auth A] K [auth A] O [auth B] CA [auth G], GA [auth H], J [auth A], K [auth A], O [auth B], P [auth B], U [auth C], V [auth C], W [auth C], X [auth C], Y [auth C]	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE C₁₆ H₃₄ O₅ FEOZZFHAVXYAMB-UHFFFAOYSA-N		Interactions Focus chain CA [auth G] Focus chain GA [auth H] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain CA [auth G] Focus chain GA [auth H] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain DA [auth H] SDF format, chain EA [auth H] SDF format, chain FA [auth H] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain IA [auth I] SDF format, chain JA [auth I] SDF format, chain M [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain Z [auth G] SDF format, chain R [auth C] SDF format, chain N [auth B] SDF format, chain L [auth B] SDF format, chain HA [auth I] SDF format, chain BA [auth G] MOL2 format, chain AA [auth G] MOL2 format, chain DA [auth H] MOL2 format, chain EA [auth H] MOL2 format, chain FA [auth H] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth I] MOL2 format, chain JA [auth I] MOL2 format, chain M [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain Z [auth G] MOL2 format, chain R [auth C] MOL2 format, chain N [auth B] MOL2 format, chain L [auth B] MOL2 format, chain HA [auth I] MOL2 format, chain BA [auth G] mmCIF format, chain AA [auth G] mmCIF format, chain DA [auth H] mmCIF format, chain EA [auth H] mmCIF format, chain FA [auth H] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth I] mmCIF format, chain JA [auth I] mmCIF format, chain M [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain Z [auth G] mmCIF format, chain R [auth C] mmCIF format, chain N [auth B] mmCIF format, chain L [auth B] mmCIF format, chain HA [auth I] mmCIF format, chain BA [auth G]	AA [auth G] BA [auth G] DA [auth H] EA [auth H] FA [auth H] AA [auth G], BA [auth G], DA [auth H], EA [auth H], FA [auth H], G [auth A], H [auth A], HA [auth I], I [auth A], IA [auth I], JA [auth I], L [auth B], M [auth B], N [auth B], R [auth C], S [auth C], T [auth C], Z [auth G]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain BA [auth G] Focus chain DA [auth H] Focus chain EA [auth H] Focus chain FA [auth H] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth I] Focus chain I [auth A] Focus chain IA [auth I] Focus chain JA [auth I] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain Z [auth G] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth G] Focus chain DA [auth H] Focus chain EA [auth H] Focus chain FA [auth H] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth I] Focus chain I [auth A] Focus chain IA [auth I] Focus chain JA [auth I] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain Z [auth G]