7EQR

Crystal structure of Truncated (Delta 1-19) Chitoporin VhChiP from Vibrio harveyi in complex with chitohexaose

PDB DOI: https://doi.org/10.2210/pdb7EQR/pdb

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

Deposited: 2021-05-04 Released: 2022-08-10
Deposition Author(s): Aunkham, A., Sanram, S., Suginta, S.
Funding Organization(s): Vidyasirimedhi Institute of Science and Technology (VISTEC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.223
R-Value Work: 0.180
R-Value Observed: 0.182

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of truncated VhChiP complex with chitohexaose

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

To be published.

Macromolecule Content

Total Structure Weight: 231.99 kDa
Atom Count: 16,450
Modelled Residue Count: 1,986
Deposited Residue Count: 1,986
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	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	L0RVU0
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G	2		N/A	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H, L	6		N/A	Interactions Focus chain H Focus chain L Interactions & Density Focus chain H Focus chain L
Glycosylation Resources
GlyTouCan: G36414FS GlyCosmos: G36414FS GlyGen: G36414FS

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I	4		N/A	Interactions Focus chain I Interactions & Density Focus chain I
Glycosylation Resources
GlyTouCan: G01361SX GlyCosmos: G01361SX GlyGen: G01361SX

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J, K	5		N/A	Interactions Focus chain J Focus chain K Interactions & Density Focus chain J Focus chain K
Glycosylation Resources
GlyTouCan: G07670VS GlyCosmos: G07670VS GlyGen: G07670VS

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
C8E Query on C8E Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain KA [auth D] SDF format, chain LA [auth D] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain PA [auth E] SDF format, chain Q [auth A] SDF format, chain QA [auth E] SDF format, chain RA [auth E] SDF format, chain SA [auth E] SDF format, chain TA [auth E] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain XA [auth F] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain KA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth E] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth E] MOL2 format, chain RA [auth E] MOL2 format, chain SA [auth E] MOL2 format, chain TA [auth E] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth F]	BA [auth C] CA [auth C] DA [auth C] EA [auth C] FA [auth C] BA [auth C], CA [auth C], DA [auth C], EA [auth C], FA [auth C], GA [auth C], HA [auth C], KA [auth D], LA [auth D], N [auth A], O [auth A], P [auth A], PA [auth E], Q [auth A], QA [auth E], RA [auth E], SA [auth E], TA [auth E], V [auth B], W [auth B], X [auth B], XA [auth F]	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE C₁₆ H₃₄ O₅ FEOZZFHAVXYAMB-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth E] Focus chain Q [auth A] Focus chain QA [auth E] Focus chain RA [auth E] Focus chain SA [auth E] Focus chain TA [auth E] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain XA [auth F] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth E] Focus chain Q [auth A] Focus chain QA [auth E] Focus chain RA [auth E] Focus chain SA [auth E] Focus chain TA [auth E] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain XA [auth F]
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A]	M [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth F] SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain OA [auth D] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain UA [auth E] SDF format, chain VA [auth E] SDF format, chain WA [auth E] SDF format, chain Y [auth B] SDF format, chain YA [auth F] SDF format, chain Z [auth B] SDF format, chain ZA [auth F] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth F] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain OA [auth D] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth E] MOL2 format, chain VA [auth E] MOL2 format, chain WA [auth E] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth F] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth F]	AA [auth B] AB [auth F] IA [auth C] JA [auth C] MA [auth D] AA [auth B], AB [auth F], IA [auth C], JA [auth C], MA [auth D], NA [auth D], OA [auth D], R [auth A], S [auth A], T [auth A], U [auth A], UA [auth E], VA [auth E], WA [auth E], Y [auth B], YA [auth F], Z [auth B], ZA [auth F]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth F] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain UA [auth E] Focus chain VA [auth E] Focus chain WA [auth E] Focus chain Y [auth B] Focus chain YA [auth F] Focus chain Z [auth B] Focus chain ZA [auth F] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth F] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain UA [auth E] Focus chain VA [auth E] Focus chain WA [auth E] Focus chain Y [auth B] Focus chain YA [auth F] Focus chain Z [auth B] Focus chain ZA [auth F]