SAXSdb — 1yfh

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

Methylated-DNA--protein-cysteine methyltransferase

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–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain C； UniProt 1–179	Not recorded	5'-D(GPTPGPGPAPTPGP(XCY)PGPTPGPTPAPGPGPT)-3' × 1 5'-D(CPCPTPAPCPAPCPAPCPAPTPCPCPAPCPA)-3' × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.7；277 K；PEG 4000, sodium chloride, citrate, magnesium chloride, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.01 Å R-free 0.286
2	Protein–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain A； UniProt 1–179	Not recorded	5'-D(GPTPGPGPAPTPGP(XCY)PGPTPGPTPAPGPGPT)-3' × 1 5'-D(CPCPTPAPCPAPCPAPCPAPTPCPCPAPCPA)-3' × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.7；277 K；PEG 4000, sodium chloride, citrate, magnesium chloride, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.01 Å R-free 0.286
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–179	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.7；277 K；PEG 4000, sodium chloride, citrate, magnesium chloride, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.01 Å R-free 0.286

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 1YFH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EH6 HUMAN O6-ALKYLGUANINE-DNA ALKYLTRANSFERASE Deposited 2000-02-18	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–207（207 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；18 MG/ML PROTEIN, 1.5 M SUCROSE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.00 Å R-free 0.218
1EH7 METHYLATED HUMAN O6-ALKYLGUANINE-DNA ALKYLTRANSFERASE Deposited 2000-02-18	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–207（207 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；18 MG/ML PROTEIN, 1.5 M SUCROSE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.229
1EH8 BENZYLATED HUMAN O6-ALKYLGUANINE-DNA ALKYLTRANSFERASE Deposited 2000-02-18	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–207（207 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；18 MG/ML PROTEIN, 1.5 M SUCROSE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.230
1QNT X-ray structure of human O6alkylguanine-DNA alkyltransferase Deposited 1999-10-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–176（176 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；1.75M (NH4)2SO4, PH 7.5	Resolution 1.90 Å R-free 0.221
1T38 HUMAN O6-ALKYLGUANINE-DNA ALKYLTRANSFERASE BOUND TO DNA CONTAINING O6-METHYLGUANINE Deposited 2004-04-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–176（176 aa）	Mutation：C145S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；PEG 3000, Tris, sodium chloride, xylitol, calcium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.20 Å R-free 0.307
1T39 HUMAN O6-ALKYLGUANINE-DNA ALKYLTRANSFERASE COVALENTLY CROSSLINKED TO DNA Deposited 2004-04-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–176（176 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 8000, MES, calcium acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.30 Å R-free 0.344
1T39 HUMAN O6-ALKYLGUANINE-DNA ALKYLTRANSFERASE COVALENTLY CROSSLINKED TO DNA Deposited 2004-04-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 1–176（176 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 8000, MES, calcium acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.30 Å R-free 0.344
28OP Structure of the human inner kinetochore CCAN and CENP-C bound to DNA Deposited 2026-02-11	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 × 16 PDB declaration: 18-meric	Chain C 1–182（182 aa） Chain T 1–182（182 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
8RGG Structure of dynein-2 intermediate chain DYNC2I2 (WDR34) in complex with dynein-2 heavy chain DYNC2H1. Deposited 2023-12-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric	Chain B 2–184（183 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
8RGH Structure of dynein-2 intermediate chain DYNC2I1 (WDR60) in complex with the dynein-2 heavy chain DYNC2H1. Deposited 2023-12-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 2–184（183 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
8RTY Structure of the F-actin barbed end bound by Cdc12 and profilin (ring complex) at a resolution of 6.3 Angstrom Deposited 2024-01-29	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 × 10 PDB declaration: decameric	Chain E 2–182（181 aa） Chain F 2–182（181 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 4 MG MAGNESIUM ION × 4 PO4 PHOSPHATE ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.1；1xKMEH (10 mM HEPES pH 7.1, 100 mM KCl, 2 mM MgCl2, 1 mM EGTA, 0.5 mM TCEP) cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；3 seconds, force 0.	Resolution 6.25 Å
8RU2 Structure of the F-actin barbed end bound by formin mDia1 Deposited 2024-01-29	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 × 5 PDB declaration: pentameric	Chain E 1–182（182 aa） Chain F 1–182（182 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.1 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；3 seconds, force 0.	Resolution 3.49 Å
9HHL Structure of Dynein-Dynactin-NuMA-LIS1 Deposited 2024-11-21	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 × 41 PDB declaration: 41-meric	Chain 1 1–182（182 aa） Chain 2 1–182（182 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 8 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.53 Å
9QEY Cryo-EM structure of the actin filament bound by a single Coronin-1B molecule. Deposited 2025-03-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain H 1–182（182 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 5 MG MAGNESIUM ION × 5 PO4 PHOSPHATE ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.1；1xKMEH (10 mM HEPES pH 7.1, 100 mM KCl, 2 mM MgCl2, 1 mM EGTA, 0.5 mM TCEP, 0.01% Tween20). cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.74 Å
9QF2 Cryo-EM structure of the fully Coronin-1B-decorated actin filament in the ADP state. Deposited 2025-03-11	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 × 10 PDB declaration: decameric	Chain F 1–182（182 aa） Chain G 1–182（182 aa） Chain H 1–182（182 aa） Chain I 1–182（182 aa） Chain J 1–182（182 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 5 MG MAGNESIUM ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.1；1xKMEH (10 mM HEPES pH 7.1, 100 mM KCl, 2 mM MgCl2, 1 mM EGTA, 0.5 mM TCEP, 0.01% Tween20). cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.42 Å
9QFB Cryo-EM structure of the fully Coronin-1B-decorated actin filament in the ADP state. Deposited 2025-03-11	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: 14-meric	Chain H 1–182（182 aa） Chain I 1–182（182 aa） Chain J 1–182（182 aa） Chain K 1–182（182 aa） Chain L 1–182（182 aa） Chain M 1–182（182 aa） Chain N 1–182（182 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 7 MG MAGNESIUM ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.1；1xKMEH (10 mM HEPES pH 7.1, 100 mM KCl, 2 mM MgCl2, 1 mM EGTA, 0.5 mM TCEP, 0.01% Tween20). cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.74 Å
9QFE Cryo-EM structure of the actin filament hetero-decorated by Coronin-1 and Cofilin-1 on separate actin strands Deposited 2025-03-11	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: 14-meric	Chain L 1–182（182 aa） Chain M 1–182（182 aa） Chain N 1–182（182 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 7 MG MAGNESIUM ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.1；1xKMEH (10 mM HEPES pH 7.1, 100 mM KCl, 2 mM MgCl2, 1 mM EGTA, 0.5 mM TCEP, 0.02% Tween20). cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.12 Å
9QFG Cryo-EM structure of the actin filament hetero-decorated by Coronin-1 and Cofilin-1, strand boundary Deposited 2025-03-11	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: 14-meric	Chain J 1–182（182 aa） Chain K 1–182（182 aa） Chain L 1–182（182 aa） Chain M 1–182（182 aa） Chain N 1–182（182 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 7 MG MAGNESIUM ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.1；1xKMEH (10 mM HEPES pH 7.1, 100 mM KCl, 2 mM MgCl2, 1 mM EGTA, 0.5 mM TCEP, 0.02% Tween20). cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.49 Å
9QFK Cryo-EM structure of the Coronin-1B-decorated actin filament bound by one Cofilin-1 molecule (crosslinked) Deposited 2025-03-11	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: 14-meric	Chain H 1–182（182 aa） Chain I 1–182（182 aa） Chain K 1–182（182 aa） Chain L 1–182（182 aa） Chain M 1–182（182 aa） Chain N 1–182（182 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 7 MG MAGNESIUM ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.1；1xKMEH (10 mM HEPES pH 7.1, 100 mM KCl, 2 mM MgCl2, 1 mM EGTA, 0.5 mM TCEP, 0.02% Tween20). cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.99 Å
9QFQ Cryo-EM structure of the cofilactin barbed end bound by AIP1 Deposited 2025-03-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 11 PDB declaration: 11-meric	Chain P 1–182（182 aa）	Not recorded	MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.1；1xKMEH (10 mM HEPES pH 7.1, 100 mM KCl, 2 mM MgCl2, 1 mM EGTA, 0.5 mM TCEP, 0.015% Tween20) cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.76 Å
9QFW Cryo-EM structure of the cofilactin barbed end bound by two AIP1 molecules Deposited 2025-03-12	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 × 12 PDB declaration: 12-meric	Chain P 1–182（182 aa） Chain Q 1–182（182 aa）	Not recorded	MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.1；1xKMEH (10 mM HEPES pH 7.1, 100 mM KCl, 2 mM MgCl2, 1 mM EGTA, 0.5 mM TCEP, 0.015% Tween20) cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.16 Å
9TAY Structure of the human inner kinetochore CCAN bound to a di-CENP-A nucleosome Deposited 2025-11-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 35 PDB declaration: 37-meric	Chain T 1–182（182 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 15.50 Å

21 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MGMT_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–179； UniProt 1–179 Author chain B； PDBConstruct 1–179； UniProt 1–179 Author chain C； PDBConstruct 1–179； UniProt 1–179

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	1yfh
Deposition date deposition_date	2004-12-31
Structure title title	wt Human O6-Alkylguanine-DNA Alkyltransferase Bound To DNA Containing an Alkylated Cytosine
Keywords keywords	protein-DNA complex, TRANSFERASE-DNA COMPLEX; TRANSFERASE/DNA
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	29.96 Å
Radius of gyration Rg (electron density) rg_electron	28.74 Å
Forward intensity I(0) i0	111003000.00
Molecular weight molecular_weight	71450.0 kDa
Excluded volume excluded_volume	84460 Å³
Envelope volume envelope_volume	115420 Å³
Hydration-shell volume shell_volume	33386 Å³
Envelope diameter envelope_diameter	95.6 Å
Shell Rg shell_rg	36.09 Å
Envelope Rg envelope_rg	27.98 Å
Shape Rg shape_rg	28.70 Å
Total Rg total_rg	29.50 Å
Total atoms total_atoms	4940
Residues n_residues	537
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	89.7 Å
Rg (real space) rg_real	29.78 Å
Rg uncertainty (real space) rg_real_error	0.36 Å
I(0) (real space) i0_real	1.1100e+08
I(0) uncertainty (real space) i0_real_error	1.2730e+06
Rg (reciprocal space) rg_reciprocal	29.86 Å
I(0) (reciprocal space) i0_reciprocal	111000000.0000
Solution quality estimate total_estimate	0.9061
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	40.6 Å
Skewness Skewness skewness	0.049
Kurtosis Kurtosis kurtosis	-0.479
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0002
Highest regularization parameter α highest_alpha	4565000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.952; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.931

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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	5'-D(GPTPGPGPAPTPGP(XCY)PGPTPGPTPAPGPGPT)-3'
Molecular weight formula_weight	5144.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D,F
Atom count atom_count	4946

GTGGATGCGTGTAGGT

Entity 2 Entity 2 polymer

Description description	5'-D(CPCPTPAPCPAPCPAPCPAPTPCPCPAPCPA)-3'
Molecular weight formula_weight	4756.1 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E,G

CCTACACACATCCACA

Entity 3 Entity 3 polymer

Description description	Methylated-DNA--protein-cysteine methyltransferase
Molecular weight formula_weight	19233.3 kDa
EC 编号 ec_number	2.1.1.63
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C

MDKDCEMKRTTLDSPLGKLELSGCEQGLHEIKLLGKGTSAADAVEVPAPAAVLGGPEPLMQCTAWLNAYFHQPEAIEEFPVPALHHPVFQQESFTRQVLWKLLKVVKFGEVISYQQLAALAGNPKAARAVGGAMRGNPVPILIPCHRVVCSSGAVGNYSGGLAVKEWLLAHEGHRLGKP

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

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	6

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1yfha1
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.4.2.1 — Methylated DNA-protein cysteine methyltransferase, C-terminal domain

Domain ID domain_id	d1yfha2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.7 — Methylated DNA-protein cysteine methyltransferase domain
Family Family family	c.55.7.1 — Methylated DNA-protein cysteine methyltransferase domain

Domain ID domain_id	d1yfhb1
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.4.2.1 — Methylated DNA-protein cysteine methyltransferase, C-terminal domain

Domain ID domain_id	d1yfhb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.7 — Methylated DNA-protein cysteine methyltransferase domain
Family Family family	c.55.7.1 — Methylated DNA-protein cysteine methyltransferase domain

Domain ID domain_id	d1yfhc1
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.4.2.1 — Methylated DNA-protein cysteine methyltransferase, C-terminal domain

Domain ID domain_id	d1yfhc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.7 — Methylated DNA-protein cysteine methyltransferase domain
Family Family family	c.55.7.1 — Methylated DNA-protein cysteine methyltransferase domain

CATH v4.4 (6 domains)

Domain ID domain_id	1yfhA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	70 — Methylated DNA-protein cysteine methyltransferase domain

Domain ID domain_id	1yfhA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	1yfhB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	70 — Methylated DNA-protein cysteine methyltransferase domain

Domain ID domain_id	1yfhB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	1yfhC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	70 — Methylated DNA-protein cysteine methyltransferase domain

Domain ID domain_id	1yfhC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

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8. Citations (1)

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Unit-cell length a length_a	58.150 Å
Unit-cell length b length_b	102.710 Å
Unit-cell length c length_c	87.940 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.77 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.010 Å
Low-resolution limit resolution_low	29.170 Å
R factor r_factor	0.2460
R_work r_work	0.2460
R_free r_free	0.2860

fit	/app/data/saxs_computation/yf/1yfh/1yfh.fit
pddf	/app/data/pr_computation/yf/1yfh/1yfh.pr.out
profile	/app/data/saxs_computation/yf/1yfh/1yfh.dat

wt Human O6-Alkylguanine-DNA Alkyltransferase Bound To DNA Containing an Alkylated Cytosine

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

Methylated-DNA--protein-cysteine methyltransferase

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

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)