2VAD: Monomeric red fluorescent protein, DsRed.M1

Name: PDB 2VAD: Monomeric red fluorescent protein, DsRed.M1
Published: 2007-11-06
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: fluorescent protein

Monomeric red fluorescent protein, DsRed.M1. Determined by X-ray diffraction at 1.59 Å resolution. Released 6 Nov 2007.

Method: X-ray diffraction
Resolution: 1.59 Å
Organism: DISCOSOMA SP.
Chains: 1
Atoms: 1,952
Mol. weight: 25.87 kDa
Ligands: ZN
Released: 6 Nov 2007

Explore 2VAD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2VAD contains 8 α-helices and 13 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	12-22	11	1
β-strand	25-36	12	1
β-strand	41-50	10	1
α-helix	52	1
α-helix	54	1
α-helix	58-60	3
α-helix	62-64	3
α-helix	70-72	3
β-strand	74	1	1
α-helix	82-85	4
β-strand	91-99	9	1
β-strand	104-114	11	1
β-strand	117-127	11	1
β-strand	140-143	4	1
α-helix	144-145	2
β-strand	146-153	8	1
β-strand	156-167	12	1
β-strand	172-183	12	1
α-helix	188-190	3
β-strand	193-204	12	1
β-strand	210-220	11	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Red fluorescent protein	A	protein	223	DISCOSOMA SP.	Q9U6Y8 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2VAD_1 RED FLUORESCENT PROTEIN (chains A)
MDNTEDVIKEFMQFKVRMEGSVNGHYFEIEGEGEGKPYEGTQTAKLQVTKGGPLPFAWDI
LSPQFQYGSKAYVKHPADIPDYMKLSFPEGFTWERSMNFEDGGVVEVQQDSSLQDGTFIY
KVKFKGVNFPADGPVMQKKTAGWEPSTEKLYPQDGVLKGEISHALKLKDGGHYTCDFKTV
YKAKKPVQLPGNHYVDSKLDITNHNEDYTVVEQYEHAEARHSGSQ

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3

Water and common crystallization additives (EDO, CL) are not listed.

Primary citation

Structural Rearrangements Near the Chromophore Influence the Maturation Speed and Brightness of Dsred Variants. Strongin, D.E., Bevis, B., Khuong, N. et al. Protein Eng Des Sel (2007) 20:525. DOI 10.1093/PROTEIN/GZM046 · PubMed

Other PDB entries of the same protein (UniProt Q9U6Y8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2H5O 1.08 Å, Crystal structure of mOrange
8B7G 1.3 Å, Structure of oxygen-degraded rsCherry
7ZCT 1.33 Å, Structure of the red fluorescent protein mScarlet3 at pH 7.5
9LSC 1.38 Å, Crystal structure of mRFP1 with a grafted calcium-binding sequence and two bound calcium…
1ZGO 1.4 Å, High Resolution Crystal Structure of the Discosoma Red Fluorescent Protein (DsRed)
7OIN 1.4 Å, Crystal structure of LSSmScarlet - a genetically encoded red fluorescent protein with a…
8ARM 1.41 Å, Crystal structure of LSSmScarlet2
8ZXH 1.46 Å, Structure of the red fluorescent protein mScarlet3-H at pH 4.5
5LK4 1.47 Å, Structure of the Red Fluorescent Protein mScarlet at pH 7.8
8B65 1.55 Å, Structure of rsCherry crystallized in anaerobic conditions
2H5R 1.6 Å, Crystal structure of mStrawberry at pH 10.5
9LSA 1.62 Å, Crystal structure of mRFP1 with a grafted calcium-binding sequence and one bound calcium…

Browse structure collections

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