8DPD | pdb_00008dpd

superfolder GFP Tyr74pCNPhe mutant

PDB DOI: https://doi.org/10.2210/pdb8DPD/pdb

Classification: FLUORESCENT PROTEIN
Organism(s): Aequorea victoria
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2022-07-15 Released: 2022-08-31
Deposition Author(s): Phillips-Piro, C.M., Papoutsis, B., Piacentini, J.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.51 Å
R-Value Free:
0.252 (Depositor), 0.250 (DCC)
R-Value Work:
0.208 (Depositor), 0.200 (DCC)
R-Value Observed:
0.210 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Superfolder GFP Tyr74pCNPhe mutant

Phillips-Piro, C.M., Papoutsis, B., Piacentini, J.

To be published.

Macromolecule Content

Total Structure Weight: 27.4 kDa
Atom Count: 2,177
Modeled Residue Count: 228
Deposited Residue Count: 237
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superfolder green fluorescent protein	A	237	Aequorea victoria	Mutation(s): 13 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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	C [auth A], D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
CO2 Query on CO2 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CARBON DIOXIDE C O₂ CURLTUGMZLYLDI-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	H [auth A], I [auth A], J [auth A], K [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
4CF Query on 4CF	A	L-PEPTIDE LINKING	C₁₀ H₁₀ N₂ O₂		PHE
CRO Query on CRO	A	L-PEPTIDE LINKING	C₁₅ H₁₇ N₃ O₅		THR, TYR, GLY