1yfh

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

Method: X-RAY DIFFRACTION

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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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 2	5'-D(GPTPGPGPAPTPGP(XCY)PGPTPGPTPAPGPGPT)-3' × 1 5'-D(CPCPTPAPCPAPCPAPCPAPTPCPCPAPCPA)-3' × 1 ZINC ION × 1 water × 1	Consistent with all polymers
2	Protein–DNA	Monomer	Protein 1 DNA 2	5'-D(GPTPGPGPAPTPGP(XCY)PGPTPGPTPAPGPGPT)-3' × 1 5'-D(CPCPTPAPCPAPCPAPCPAPTPCPCPAPCPA)-3' × 1 ZINC ION × 1 water × 2	Consistent with all polymers
3	Protein monomer	Monomer	Protein 1	ZINC ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

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. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1yfh__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1yfh__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1yfh__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	21.01 Å
Rg (electron density)	19.83 Å
Total Rg	20.66 Å
Atom count	1805
Residues	180
Excluded volume	30285 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1yfh__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1yfh__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1yfh__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. 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

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism 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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6. 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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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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1yfh__assembly_1__model_1

1yfh__assembly_1__model_1 | I(q)

1yfh__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. 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

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1yfh__assembly_1__model_1

1yfh__assembly_1__model_1 | I(q)

1yfh__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. 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

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)