7YZW | pdb_00007yzw

Llama nanobody VHH15 raised against the glycoprotein of Ebola virus

PDB DOI: https://doi.org/10.2210/pdb7YZW/pdb

Classification: IMMUNE SYSTEM
Organism(s): Lama glama
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-02-21 Released: 2023-03-01
Deposition Author(s): Coulibaly, A.B., Roussel, A., Leone, P.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.213 (Depositor), 0.210 (DCC)
R-Value Work:
0.190 (Depositor), 0.180 (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 1.2 of the entry. See complete history.

Literature

Structural characterization of a nanobody raised against the Ebola virus glycoprotein

Coulibaly, A.B., Amigues, B., Imbert, I., Roussel, A., Leone, P.

To be published.

Macromolecule Content

Total Structure Weight: 90.19 kDa
Atom Count: 6,823
Modeled Residue Count: 740
Deposited Residue Count: 792
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
nanobody	A, B, C, D, E A, B, C, D, E, F	132	Lama glama	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CXS Query on CXS Download Ideal Coordinates CCD File SDF format, chain R [auth F] MOL2 format, chain R [auth F] mmCIF format, chain R [auth F]	R [auth F]	3-CYCLOHEXYL-1-PROPYLSULFONIC ACID C₉ H₁₉ N O₃ S PJWWRFATQTVXHA-UHFFFAOYSA-N		Interactions Focus chain R [auth F] Interactions & Density Focus chain R [auth F]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain S [auth F] SDF format, chain T [auth F] SDF format, chain U [auth F] MOL2 format, chain G [auth A] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain S [auth F] MOL2 format, chain T [auth F] MOL2 format, chain U [auth F] mmCIF format, chain G [auth A] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain P [auth D] mmCIF format, chain S [auth F] mmCIF format, chain T [auth F] mmCIF format, chain U [auth F]	G [auth A] K [auth C] L [auth C] M [auth C] N [auth C] G [auth A], K [auth C], L [auth C], M [auth C], N [auth C], P [auth D], S [auth F], T [auth F], U [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D] Focus chain S [auth F] Focus chain T [auth F] Focus chain U [auth F] Interactions & Density Focus chain G [auth A] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D] Focus chain S [auth F] Focus chain T [auth F] Focus chain U [auth F]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain J [auth C] SDF format, chain O [auth D] SDF format, chain Q [auth E] SDF format, chain H [auth B] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] MOL2 format, chain O [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain H [auth B] mmCIF format, chain I [auth C] mmCIF format, chain J [auth C] mmCIF format, chain O [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain H [auth B]	H [auth B], I [auth C], J [auth C], O [auth D], Q [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain O [auth D] Focus chain Q [auth E] Interactions & Density Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain O [auth D] Focus chain Q [auth E]