5NI3

sfGFP 204-204 mutant dimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Association of Fluorescent Protein Pairs and Its Significant Impact on Fluorescence and Energy Transfer

Pope, J.R.Johnson, R.L.Jamieson, W.D.Worthy, H.L.Kailasam, S.Ahmed, R.D.Taban, I.Auhim, H.S.Watkins, D.W.Rizkallah, P.J.Castell, O.K.Jones, D.D.

(2020) Adv Sci (Weinh) 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Green fluorescent proteinA225Aequorea victoriaMutation(s): 2 
Gene Names: GFP
UniProt
Find proteins for P42212 (Aequorea victoria)
Explore P42212 
Go to UniProtKB:  P42212
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Green fluorescent proteinB229Aequorea victoriaMutation(s): 2 
Gene Names: GFP
UniProt
Find proteins for P42212 (Aequorea victoria)
Explore P42212 
Go to UniProtKB:  P42212
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Green fluorescent proteinC, D229Aequorea victoriaMutation(s): 1 
Gene Names: GFP
UniProt
Find proteins for P42212 (Aequorea victoria)
Explore P42212 
Go to UniProtKB:  P42212
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DB5 (Subject of Investigation/LOI)
Query on DB5

Download Ideal Coordinates CCD File 
G [auth A], L [auth B][(4~{S})-4,5,6,7,8,9-hexahydro-1~{H}-cycloocta[d][1,2,3]triazol-4-yl] hydrogen carbonate
C9 H13 N3 O3
ZBJGIWFCJONVKZ-ZETCQYMHSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth B], I [auth B], J [auth B], M [auth C], R [auth D]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
Q [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth A] , F [auth A] , K [auth B] , N [auth C] , O [auth C] , P [auth C] , S [auth D] , T [auth D] , 
E [auth A],  F [auth A],  K [auth B],  N [auth C],  O [auth C],  P [auth C],  S [auth D],  T [auth D],  U [auth D],  V [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CRO
Query on CRO
AL-PEPTIDE LINKINGC15 H17 N3 O5THR, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.7α = 90
b = 98.02β = 90
c = 102.64γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-12
    Type: Initial release
  • Version 1.1: 2019-02-20
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.2: 2019-07-10
    Changes: Data collection
  • Version 1.3: 2019-10-16
    Changes: Data collection
  • Version 1.4: 2020-03-25
    Changes: Database references
  • Version 1.5: 2020-12-02
    Changes: Database references, Derived calculations