6Y8P: O6-alkylguanine-DNA alkyltransferase mutant

Name: PDB 6Y8P: Crystal structure of SNAP-tag labeled with a benzyl-tetramethylrhodamine fluorophore
Published: 2021-03-31
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Crystal structure of SNAP-tag labeled with a benzyl-tetramethylrhodamine fluorophore. Determined by X-ray diffraction at 2.3 Å resolution. Released 31 Mar 2021.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,326
Mol. weight: 19.61 kDa
Ligands: ZN, OGQ
Released: 31 Mar 2021

Explore 6Y8P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6Y8P contains 9 α-helices and 10 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: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	8-10	3	1
β-strand	13-15	3	2
β-strand	17-18	2	2
β-strand	19-23	5	1
β-strand	28-33	6	1
α-helix	57-71	15
α-helix	73-78	6
α-helix	80-83	4
β-strand	84	1	1
α-helix	87-89	3
α-helix	94-105	12
β-strand	112-113	2	3
α-helix	114-120	7
α-helix	127-135	9
β-strand	140	1	4
β-strand	143	1	4
α-helix	145-147	3
β-strand	148-149	2	3
α-helix	162-171	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
O6-alkylguanine-DNA alkyltransferase mutant	A	protein	177	Homo sapiens	E5BBQ0 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6Y8P_1 O6-alkylguanine-DNA alkyltransferase mutant (chains A)
GDCEMKRTTLDSPLGKLELSGCEQGLHEIIFLGKGTSAADAVEVPAPAAVLGGPEPLMQA
TAWLNAYFHQPEAIEEFPVPALHHPVFQQESFTRQVLWKLLKVVKFGEVISYSHLAALAG
NPAATAAVKTALSGNPVPILIPCHRVVQGDLDVGGYEGGLAVKEWLLAHEGHRLGKR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
OGQ	[9-[2-carboxy-5-[(4-methylphenyl)methylcarbamoyl]phenyl]-6-(dimethylamino)xanth…	C33 H32 N3 O4	1

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

Primary citation

Kinetic and Structural Characterization of the Self-Labeling Protein Tags HaloTag7, SNAP-tag, and CLIP-tag. Wilhelm, J., Kuhn, S., Tarnawski, M. et al. Biochemistry (2021) 60:2560-2575. DOI 10.1021/acs.biochem.1c00258 · PubMed

Other PDB entries of the same protein (UniProt E5BBQ0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3KZY 1.9 Å, Crystal structure of SNAP-tag
8TK7 2.53 Å, Myxococcus xanthus EncA protein shell with compartmentalized SNAP-tag cargo protein
9Q2H 2.74 Å, Rad55-Rad57-SHU homologous recombination complex
9Q2I 3.0 Å, Rad55-Rad57-SHU homologous recombination complex
9Q2C 3.06 Å, Rad55-Rad57-SHU-Rad51 bound to ssDNA with AMP-PNP
9Q2F 3.06 Å, Rad55-Rad57-SHU-Rad51-Rad51 bound to ssDNA with AMP-PNP
8DD7 3.3 Å, The Cryo-EM structure of Drosophila Cryptochrome in complex with Timeless
9Q2E 3.44 Å, Rad55-Rad57-SHU bound to ssDNA
9Q2L 3.7 Å, Rad55-Rad57(E161Q)-SHU-3xRad51 bound to ssDNA with ATP
6RLA 3.9 Å, Structure of the dynein-2 complex; motor domains
6SC2 3.9 Å, Structure of the dynein-2 complex; IFT-train bound model
6RLB 4.5 Å, Structure of the dynein-2 complex; tail domain

Browse structure collections

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