8F65 | pdb_00008f65

Crystal structure of VACV D13 in complex with BBL030900

PDB DOI: https://doi.org/10.2210/pdb8F65/pdb

Classification: VIRAL PROTEIN
Organism(s): Orthopoxvirus vaccinia
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2022-11-16 Released: 2023-12-13
Deposition Author(s): Subedi, B.P., Garriga, D., Coulibaly, F.
Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free:
0.239 (Depositor), 0.239 (DCC)
R-Value Work:
0.173 (Depositor), 0.174 (DCC)
R-Value Observed:
0.176 (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 of scaffolidng protein D13 of Vaccinia Virus in complex with fragments inhibiting A17 binding.

Subedi, B.P., Garriga, D., Coulibaly, F.

To be published.

Macromolecule Content

Total Structure Weight: 196.75 kDa
Atom Count: 13,277
Modeled Residue Count: 1,617
Deposited Residue Count: 1,728
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Scaffold protein D13	A, B, C	576	Orthopoxvirus vaccinia	Mutation(s): 0 Gene Names: VACWR118, D13L
UniProt
Find proteins for P68440 (Vaccinia virus (strain Western Reserve)) Explore P68440 Go to UniProtKB: P68440
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68440
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QF6 (Subject of Investigation/LOI) Query on QF6 Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain Y [auth B]	Y [auth B]	8-methoxyquinolin-4-amine C₁₀ H₁₀ N₂ O QMBPJEIUEYDRGP-UHFFFAOYSA-N		Interactions Focus chain Y [auth B] Interactions & Density Focus chain Y [auth B]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain D [auth A] SDF format, chain DA [auth C] SDF format, chain E [auth A] SDF format, chain EA [auth C] SDF format, chain F [auth A] SDF format, chain FA [auth C] SDF format, chain G [auth A] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain I [auth A] SDF format, chain IA [auth C] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Z [auth C] SDF format, chain H [auth A] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain D [auth A] MOL2 format, chain DA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Z [auth C] MOL2 format, chain H [auth A] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain D [auth A] mmCIF format, chain DA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Z [auth C] mmCIF format, chain H [auth A]	AA [auth C] BA [auth C] CA [auth C] D [auth A] DA [auth C] AA [auth C], BA [auth C], CA [auth C], D [auth A], DA [auth C], E [auth A], EA [auth C], F [auth A], FA [auth C], G [auth A], GA [auth C], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Z [auth C]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain D [auth A] Focus chain DA [auth C] Focus chain E [auth A] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain D [auth A] Focus chain DA [auth C] Focus chain E [auth A] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Z [auth C]