5M7Q | pdb_00005m7q

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 (Depositor), 0.250 (DCC)
R-Value Work:
0.196 (Depositor), 0.210 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 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
Modeled Residue Count: 250
Deposited Residue Count: 274
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 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 I [auth A] SDF format, chain C [auth B] MOL2 format, chain I [auth A] MOL2 format, chain C [auth B] mmCIF format, chain I [auth A] mmCIF format, chain C [auth B]	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 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] SDF format, chain E [auth B] MOL2 format, chain D [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] MOL2 format, chain E [auth B] mmCIF format, chain D [auth B] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain E [auth B]	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] mmCIF format, chain H [auth B] mmCIF 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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.249 (Depositor), 0.250 (DCC)
R-Value Work: 0.196 (Depositor), 0.210 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.058	α = 90
b = 49.058	β = 90
c = 225.735	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2016-11-09

Deposition Author(s):

Soler, N.

Kunz, P.

Muyldermans, S.

Revision History (Full details and data files)

Version 1.0: 2016-11-09
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-09
Changes: Structure summary