5M7Q

Engineering the Thermostability of Nanobodies - NbD2

PDB DOI: https://doi.org/10.2210/pdb5M7Q/pdb

Classification: IMMUNE SYSTEM
Organism(s): Camelus dromedarius
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-10-28 Released: 2016-11-09
Deposition Author(s): Soler, N., Kunz, P., Muyldermans, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.249
R-Value Work: 0.196
R-Value Observed: 0.198

wwPDB Validation 3D Report Full Report

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

Literature

Engineering the Thermostability of Nanobodies

Kunz, P., Flock, T., Soler, N., Zaiss, M., Vincke, C., Sterckx, Y., Muyldermans, S., Kastelic, D., Hoheisel, J.

To be published.

Macromolecule Content

Total Structure Weight: 30.58 kDa
Atom Count: 2,098
Modelled Residue Count: 250
Deposited Residue Count: 274
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody NbD2	A [auth B], B [auth A]	137	Camelus dromedarius	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
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain I [auth A] MOL2 format, chain C [auth B] MOL2 format, chain I [auth A]	C [auth B], I [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth B] Focus chain I [auth A] Interactions & Density Focus chain C [auth B] Focus chain I [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A]	D [auth B] E [auth B] F [auth B] G [auth B] J [auth A] D [auth B], E [auth B], F [auth B], G [auth B], J [auth A], K [auth A], L [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain M [auth A] MOL2 format, chain H [auth B] MOL2 format, chain M [auth A]	H [auth B], M [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain M [auth A] Interactions & Density Focus chain H [auth B] Focus chain M [auth A]