SAXSdb — 6y8p

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1. Protein Identity and Related Structures Protein Identity & Related Structures

O6-alkylguanine-DNA alkyltransferase mutant

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 7–182	Not recorded	ZN ZINC ION × 1 OGQ [9-[2-carboxy-5-[(4-methylphenyl)methylcarbamoyl]phenyl]-6-(dimethylamino)xanthen-3-ylidene]-dimethyl-azanium × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；100 mM Na HEPES pH 7.5 25% PEG 8000 10 mg/mL protein 100 nl:100 nL	Resolution 2.30 Å R-free 0.277

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6Y8P	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3KZY Crystal structure of SNAP-tag Deposited 2009-12-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–182（182 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；34% PEG 3350, 100mM BisTris pH 5.5, 500mM NaCl , VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.90 Å R-free 0.261
3KZY Crystal structure of SNAP-tag Deposited 2009-12-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–182（182 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；34% PEG 3350, 100mM BisTris pH 5.5, 500mM NaCl , VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.90 Å R-free 0.261
6RLA Structure of the dynein-2 complex; motor domains Deposited 2019-05-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 5–181（177 aa） Chain B 5–181（177 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
6RLB Structure of the dynein-2 complex; tail domain Deposited 2019-05-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain A 5–181（177 aa） Chain B 5–181（177 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.50 Å
6SC2 Structure of the dynein-2 complex; IFT-train bound model Deposited 2019-07-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain A 5–181（177 aa） Chain B 5–181（177 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
8DD7 The Cryo-EM structure of Drosophila Cryptochrome in complex with Timeless Deposited 2022-06-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–181（181 aa） Chain B 5–181（177 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.30 Å
8TK7 Myxococcus xanthus EncA protein shell with compartmentalized SNAP-tag cargo protein Deposited 2023-07-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 360 PDB declaration: 360-meric	Chain D 1–182（182 aa） Chain E 1–182（182 aa） Chain F 1–182（182 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；150 mM NaCl, 20 mM Tris pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.53 Å
8TK7 Myxococcus xanthus EncA protein shell with compartmentalized SNAP-tag cargo protein Deposited 2023-07-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 1–182（182 aa） Chain E 1–182（182 aa） Chain F 1–182（182 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；150 mM NaCl, 20 mM Tris pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.53 Å
8TK7 Myxococcus xanthus EncA protein shell with compartmentalized SNAP-tag cargo protein Deposited 2023-07-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric	Chain D 1–182（182 aa） Chain E 1–182（182 aa） Chain F 1–182（182 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；150 mM NaCl, 20 mM Tris pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.53 Å
8TK7 Myxococcus xanthus EncA protein shell with compartmentalized SNAP-tag cargo protein Deposited 2023-07-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain D 1–182（182 aa） Chain E 1–182（182 aa） Chain F 1–182（182 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；150 mM NaCl, 20 mM Tris pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.53 Å
8TK7 Myxococcus xanthus EncA protein shell with compartmentalized SNAP-tag cargo protein Deposited 2023-07-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 1–182（182 aa） Chain E 1–182（182 aa） Chain F 1–182（182 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；150 mM NaCl, 20 mM Tris pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.53 Å
9DI0 Cryo-EM structure of Kif18A bound to a microtubule Deposited 2024-09-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 5–181（177 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 TA1 TAXOL × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å

7 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	E5BBQ0_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–177； UniProt 7–182

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6y8p
Deposition date deposition_date	2020-03-05
Structure title title	Crystal structure of SNAP-tag labeled with a benzyl-tetramethylrhodamine fluorophore
Keywords keywords	SNAP-tag, self-labeling protein, tetramethylrhodamine, synthetic fluorophore, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	16.65 Å
Radius of gyration Rg (electron density) rg_electron	15.12 Å
Forward intensity I(0) i0	5704770.00
Molecular weight molecular_weight	17836.0 kDa
Excluded volume excluded_volume	22559 Å³
Envelope volume envelope_volume	25356 Å³
Hydration-shell volume shell_volume	14145 Å³
Envelope diameter envelope_diameter	54.3 Å
Shell Rg shell_rg	21.00 Å
Envelope Rg envelope_rg	15.36 Å
Shape Rg shape_rg	15.09 Å
Total Rg total_rg	16.34 Å
Total atoms total_atoms	1283
Residues n_residues	158
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	53.2 Å
Rg (real space) rg_real	16.53 Å
Rg uncertainty (real space) rg_real_error	0.28 Å
I(0) (real space) i0_real	5.7050e+06
I(0) uncertainty (real space) i0_real_error	6.3530e+04
Rg (reciprocal space) rg_reciprocal	16.55 Å
I(0) (reciprocal space) i0_reciprocal	5705000.0000
Solution quality estimate total_estimate	0.8149
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	52.5 Å
Skewness Skewness skewness	0.061
Kurtosis Kurtosis kurtosis	-0.473
Angular range angular_range	— – 0.4800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	987100.0000
Real-space data points n_real_points	78
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.866; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	O6-alkylguanine-DNA alkyltransferase mutant
Molecular weight formula_weight	18951.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1374

GDCEMKRTTLDSPLGKLELSGCEQGLHEIIFLGKGTSAADAVEVPAPAAVLGGPEPLMQATAWLNAYFHQPEAIEEFPVPALHHPVFQQESFTRQVLWKLLKVVKFGEVISYSHLAALAGNPAATAAVKTALSGNPVPILIPCHRVVQGDLDVGGYEGGLAVKEWLLAHEGHRLGKR

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	[9-[2-carboxy-5-[(4-methylphenyl)methylcarbamoyl]phenyl]-6-(dimethylamino)xanthen-3-ylidene]-dimethyl-azanium
Molecular weight formula_weight	534.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	50

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7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d6y8pa1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.2 — Methylated DNA-protein cysteine methyltransferase, C-terminal domain
Family Family family	a.4.2.0 — automated matches

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8. Citations (2)

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Unit-cell length a length_a	65.515 Å
Unit-cell length b length_b	65.515 Å
Unit-cell length c length_c	97.067 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	48.980 Å
R factor r_factor	0.2374
R_work r_work	0.2356
R_free r_free	0.2767

fit	/app/data/saxs_computation/y8/6y8p/6y8p.fit
pddf	/app/data/pr_computation/y8/6y8p/6y8p.pr.out
profile	/app/data/saxs_computation/y8/6y8p/6y8p.dat

Crystal structure of SNAP-tag labeled with a benzyl-tetramethylrhodamine fluorophore

1. Protein Identity and Related Structures Protein Identity & Related Structures

O6-alkylguanine-DNA alkyltransferase mutant

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction