8SFS

High Affinity nanobodies against GFP

PDB DOI: https://doi.org/10.2210/pdb8SFS/pdb

Classification: IMMUNE SYSTEM
Organism(s): Aequorea victoria, Lama glama
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-04-11 Released: 2024-05-22
Deposition Author(s): Ketaren, N.E., Rout, M.P., Bonnano, J.B., Almo, S.C.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.37 Å
R-Value Free: 0.218
R-Value Work: 0.190
R-Value Observed: 0.191

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

High Affinity nanobodies against GFP

Ketaren, N.E., Rout, M.P., Almo, S.

To be published.

Macromolecule Content

Total Structure Weight: 92.22 kDa
Atom Count: 5,907
Modelled Residue Count: 710
Deposited Residue Count: 802
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein	A, B	253	Aequorea victoria	Mutation(s): 1 Gene Names: GFP
UniProt
Find proteins for P42212 (Aequorea victoria) Explore P42212 Go to UniProtKB: P42212
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P42212
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LaG16	C [auth D], D [auth C]	148	Lama glama	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain L [auth B] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain X [auth D] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain L [auth B] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D]	EA [auth C] FA [auth C] GA [auth C] L [auth B] V [auth D] EA [auth C], FA [auth C], GA [auth C], L [auth B], V [auth D], W [auth D], X [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain L [auth B] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain L [auth B] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain J [auth A] SDF format, chain JA [auth C] SDF format, chain KA [auth C] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain Z [auth D]	AA [auth D] BA [auth D] CA [auth D] DA [auth D] HA [auth C] AA [auth D], BA [auth D], CA [auth D], DA [auth D], HA [auth C], IA [auth C], J [auth A], JA [auth C], KA [auth C], Z [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain Z [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain LA [auth C] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain K [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B]	K [auth A], LA [auth C], R [auth B], S [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Focus chain LA [auth C] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain K [auth A] Focus chain LA [auth C] Focus chain R [auth B] Focus chain S [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain MA [auth C] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain MA [auth C] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B]	MA [auth C], T [auth B], U [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain MA [auth C] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain MA [auth C] Focus chain T [auth B] Focus chain U [auth B]
NH4 Query on NH4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain Y [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain Y [auth D]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], Y [auth D]	AMMONIUM ION H₄ N QGZKDVFQNNGYKY-UHFFFAOYSA-O		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain Y [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain Y [auth D]