9F23

DARPin eGFP complex DP2 (2G156)

PDB DOI: https://doi.org/10.2210/pdb9F23/pdb

Classification: PROTEIN BINDING
Organism(s): Aequorea victoria, synthetic construct
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-04-22 Released: 2024-10-23
Deposition Author(s): Mittl, P.R., Hansen, S.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free: 0.212
R-Value Work: 0.174
R-Value Observed: 0.176

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

DARPin eGFP complex DP2 (2G156)

Winkelvoss, D., Pluckthun, A.

To be published.

Macromolecule Content

Total Structure Weight: 84.73 kDa
Atom Count: 6,867
Modelled Residue Count: 704
Deposited Residue Count: 742
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, C	243	Aequorea victoria	Mutation(s): 3 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

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DARPin DP2	B, D	128	synthetic construct	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
PXN Query on PXN Download Ideal Coordinates CCD File SDF format, chain R [auth C] MOL2 format, chain R [auth C] mmCIF format, chain R [auth C]	R [auth C]	(2S)-1-[3-{[(2R)-2-hydroxypropyl]oxy}-2,2-bis({[(2R)-2-hydroxypropyl]oxy}methyl)propoxy]propan-2-ol C₁₇ H₃₆ O₈ GXEZGLLPFFKHGE-FPCVCCKLSA-N		Interactions Focus chain R [auth C] Interactions & Density Focus chain R [auth C]
A1H87 Query on A1H87 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain Q [auth C] MOL2 format, chain E [auth A] MOL2 format, chain Q [auth C] mmCIF format, chain E [auth A] mmCIF format, chain Q [auth C]	E [auth A], Q [auth C]	2-[[(2S)-2-oxidanylpropoxy]methyl]-2-[[(2S)-2-[(2S)-2-oxidanylpropoxy]propoxy]methyl]propane-1,3-diol C₁₄ H₃₀ O₇ GYGFRXYZKNFZRH-AVGNSLFASA-N		Interactions Focus chain E [auth A] Focus chain Q [auth C] Interactions & Density Focus chain E [auth A] Focus chain Q [auth C]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain BA [auth D] SDF format, chain DA [auth D] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain CA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain CA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	BA [auth D] CA [auth D] DA [auth D] N [auth B] O [auth B] BA [auth D], CA [auth D], DA [auth D], N [auth B], O [auth B], P [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain AA [auth D] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain K [auth B] MOL2 format, chain AA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain K [auth B] mmCIF format, chain AA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D]	AA [auth D] F [auth A] G [auth A] H [auth A] J [auth B] AA [auth D], F [auth A], G [auth A], H [auth A], J [auth B], K [auth B], L [auth B], M [auth B], S [auth C], T [auth C], U [auth C], V [auth C], W [auth C], Y [auth D], Z [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain Y [auth D] Focus chain Z [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain X [auth C] MOL2 format, chain I [auth A] MOL2 format, chain X [auth C] mmCIF format, chain I [auth A] mmCIF format, chain X [auth C]	I [auth A], X [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain X [auth C] Interactions & Density Focus chain I [auth A] Focus chain X [auth C]