8XWO

Vibrio harveyi chitoporin in complex with minocycline

PDB DOI: https://doi.org/10.2210/pdb8XWO/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Vibrio harveyi
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-01-16 Released: 2025-01-22
Deposition Author(s): Sanram, S., Suginta, W., Robinson, R.C.
Funding Organization(s): Vidyasirimedhi Institute of Science and Technology (VISTEC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free: 0.262
R-Value Work: 0.182
R-Value Observed: 0.186

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

VhChiP in complex with minocycline

Sanram, S., Suginta, W., Robinson, R.C.

To be published.

Macromolecule Content

Total Structure Weight: 235.1 kDa
Atom Count: 15,612
Modelled Residue Count: 1,986
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, E A, B, C, D, E, F	350	Vibrio harveyi	Mutation(s): 0 Gene Names: chiP, AL538_13355, VCHENC02_0932
UniProt
Find proteins for A0A454DK07 (Vibrio harveyi) Explore A0A454DK07 Go to UniProtKB: A0A454DK07
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A454DK07
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MIY (Subject of Investigation/LOI) Query on MIY Download Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain G [auth A] SDF format, chain U [auth D] MOL2 format, chain CA [auth F] MOL2 format, chain G [auth A] MOL2 format, chain U [auth D] mmCIF format, chain CA [auth F] mmCIF format, chain G [auth A] mmCIF format, chain U [auth D]	CA [auth F], G [auth A], U [auth D]	(4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2- CARBOXAMIDE C₂₃ H₂₇ N₃ O₇ DYKFCLLONBREIL-KVUCHLLUSA-N		Interactions Focus chain CA [auth F] Focus chain G [auth A] Focus chain U [auth D] Interactions & Density Focus chain CA [auth F] Focus chain G [auth A] Focus chain U [auth D]
C8E (Subject of Investigation/LOI) Query on C8E Download Ideal Coordinates CCD File SDF format, chain DA [auth F] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain V [auth D] MOL2 format, chain DA [auth F] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain V [auth D] mmCIF format, chain DA [auth F] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain V [auth D]	DA [auth F] H [auth A] I [auth A] M [auth B] N [auth B] DA [auth F], H [auth A], I [auth A], M [auth B], N [auth B], Q [auth C], V [auth D]	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE C₁₆ H₃₄ O₅ FEOZZFHAVXYAMB-UHFFFAOYSA-N		Interactions Focus chain DA [auth F] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain V [auth D] Interactions & Density Focus chain DA [auth F] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain V [auth D]
NA (Subject of Investigation/LOI) Query on NA Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain BA [auth E] SDF format, chain EA [auth F] SDF format, chain FA [auth F] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain Z [auth E] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain FA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth E] mmCIF format, chain AA [auth E] mmCIF format, chain BA [auth E] mmCIF format, chain EA [auth F] mmCIF format, chain FA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth E]	AA [auth E] BA [auth E] EA [auth F] FA [auth F] J [auth A] AA [auth E], BA [auth E], EA [auth F], FA [auth F], J [auth A], K [auth A], L [auth A], O [auth B], P [auth B], R [auth C], S [auth C], T [auth C], W [auth D], X [auth D], Y [auth D], Z [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth E]