7X5P | pdb_00007x5p

Truncated VhChiP (1-19aa) in complex with doxycycline

PDB DOI: https://doi.org/10.2210/pdb7X5P/pdb

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

Deposited: 2022-03-05 Released: 2023-03-08
Deposition Author(s): Sanram, S., Robinson, C.R., Aunkham, A., Suginta, W.
Funding Organization(s): Vidyasirimedhi Institute of Science and Technology (VISTEC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free:
0.258 (Depositor), 0.257 (DCC)
R-Value Work:
0.182 (Depositor), 0.182 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure and function of truncated VhChiP

Aunkham, A., Sanram, S., Suginta, W.

To be published.

Macromolecule Content

Total Structure Weight: 225.56 kDa
Atom Count: 15,743
Modeled Residue Count: 1,986
Deposited Residue Count: 1,986
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, D, E A, B, C, D, E, F	331	Vibrio harveyi	Mutation(s): 0 Gene Names: chiP 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
DXT Query on DXT Download:Ideal Coordinates CCD File SDF format, chain IA [auth F] SDF format, chain Y [auth D] SDF format, chain O [auth B] SDF format, chain G [auth A] MOL2 format, chain IA [auth F] MOL2 format, chain Y [auth D] MOL2 format, chain O [auth B] MOL2 format, chain G [auth A] mmCIF format, chain IA [auth F] mmCIF format, chain Y [auth D] mmCIF format, chain O [auth B] mmCIF format, chain G [auth A]	G [auth A], IA [auth F], O [auth B], Y [auth D]	(4S,4AR,5S,5AR,6R,12AS)-4-(DIMETHYLAMINO)-3,5,10,12,12A-PENTAHYDROXY-6-METHYL-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE C₂₂ H₂₄ N₂ O₈ JBIWCJUYHHGXTC-AKNGSSGZSA-N		Interactions Focus chain G [auth A] Focus chain IA [auth F] Focus chain O [auth B] Focus chain Y [auth D] Interactions & Density Focus chain G [auth A] Focus chain IA [auth F] Focus chain O [auth B] Focus chain Y [auth D]
C8E (Subject of Investigation/LOI) Query on C8E Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain EA [auth E] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain JA [auth F] SDF format, chain K [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain U [auth C] SDF format, chain Z [auth D] SDF format, chain MA [auth F] SDF format, chain LA [auth F] SDF format, chain KA [auth F] SDF format, chain I [auth A] MOL2 format, chain AA [auth D] MOL2 format, chain EA [auth E] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth F] MOL2 format, chain K [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain U [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain MA [auth F] MOL2 format, chain LA [auth F] MOL2 format, chain KA [auth F] MOL2 format, chain I [auth A] mmCIF format, chain AA [auth D] mmCIF format, chain EA [auth E] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth F] mmCIF format, chain K [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain U [auth C] mmCIF format, chain Z [auth D] mmCIF format, chain MA [auth F] mmCIF format, chain LA [auth F] mmCIF format, chain KA [auth F] mmCIF format, chain I [auth A]	AA [auth D] EA [auth E] H [auth A] I [auth A] J [auth A] AA [auth D], EA [auth E], H [auth A], I [auth A], J [auth A], JA [auth F], K [auth A], KA [auth F], LA [auth F], MA [auth F], P [auth B], Q [auth B], R [auth B], U [auth C], Z [auth D]	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE C₁₆ H₃₄ O₅ FEOZZFHAVXYAMB-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain EA [auth E] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth F] Focus chain K [auth A] Focus chain KA [auth F] Focus chain LA [auth F] Focus chain MA [auth F] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain EA [auth E] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth F] Focus chain K [auth A] Focus chain KA [auth F] Focus chain LA [auth F] Focus chain MA [auth F] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain Z [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain DA [auth D] SDF format, chain HA [auth E] SDF format, chain L [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth F] SDF format, chain OA [auth F] SDF format, chain V [auth C] SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain M [auth A] SDF format, chain GA [auth E] SDF format, chain FA [auth E] SDF format, chain CA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain HA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth F] MOL2 format, chain OA [auth F] MOL2 format, chain V [auth C] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain M [auth A] MOL2 format, chain GA [auth E] MOL2 format, chain FA [auth E] MOL2 format, chain CA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain HA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth F] mmCIF format, chain OA [auth F] mmCIF format, chain V [auth C] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain M [auth A] mmCIF format, chain GA [auth E] mmCIF format, chain FA [auth E] mmCIF format, chain CA [auth D]	BA [auth D] CA [auth D] DA [auth D] FA [auth E] GA [auth E] BA [auth D], CA [auth D], DA [auth D], FA [auth E], GA [auth E], HA [auth E], L [auth A], M [auth A], N [auth A], NA [auth F], OA [auth F], S [auth B], T [auth B], V [auth C], W [auth C], X [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth F] Focus chain OA [auth F] Focus chain S [auth B] Focus chain T [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth F] Focus chain OA [auth F] Focus chain S [auth B] Focus chain T [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C]