1YFH: Wt Human O6-Alkylguanine-DNA Alkyltransferase

wt Human O6-Alkylguanine-DNA Alkyltransferase Bound To DNA Containing an Alkylated Cytosine. Determined by X-ray diffraction at 3.01 Å resolution. Released 13 Dec 2005.

Method: X-ray diffraction
Resolution: 3.01 Å
Organism: Homo sapiens
Chains: 7
Atoms: 4,946
Mol. weight: 77.7 kDa
Ligands: ZN
Released: 13 Dec 2005

Explore 1YFH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1YFH contains 26 α-helices and 26 β-strands across 3 chains. 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: 10 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	8-14	7	1
β-strand	17-23	7	1
β-strand	28-33	6	1
α-helix	47-49	3
β-strand	50	1	1
α-helix	51	1
α-helix	57-71	15
α-helix	75-77	3
α-helix	80-83	4
β-strand	84	1	1
α-helix	87-90	4
α-helix	94-105	12
β-strand	112-113	2	2
α-helix	114-121	8
α-helix	127-135	9
β-strand	148-149	2	2
α-helix	162-171	10
β-strand	175	1	3
β-strand	178	1	3

Chain B: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	8-14	7	4
β-strand	17-23	7	4
β-strand	28-33	6	4
β-strand	50-51	2	4
α-helix	57-71	15
α-helix	73-75	3
α-helix	80-83	4
β-strand	84	1	4
α-helix	87-90	4
α-helix	94-104	11
β-strand	112-113	2	5
α-helix	114-121	8
α-helix	127-136	10
β-strand	140	1	6
β-strand	143	1	6
β-strand	148-149	2	5
α-helix	162-171	10

Chain C: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	8-14	7	7
β-strand	17-23	7	7
β-strand	28-33	6	7
α-helix	57-71	15
α-helix	75-78	4
α-helix	80-83	4
β-strand	84	1	7
α-helix	87-90	4
α-helix	94-105	12
β-strand	112-113	2	8
α-helix	114-121	8
α-helix	127-136	10
β-strand	140	1	9
β-strand	143	1	9
β-strand	148-149	2	8
α-helix	162-171	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
5'-d(gptpgpgpaptpgp(xcy)pgptpgptpapgpgpt)-3'	D, F	DNA	16
5'-d(cpcptpapcpapcpapcpaptpcpcpapcpa)-3'	E, G	DNA	16
Methylated-DNA--protein-cysteine methyltransferase	A, B, C	protein	179	Homo sapiens	P16455 (AlphaFold model)

Sequence of entity 1 (D, F), FASTA

>1YFH_1 5'-D(*GP*TP*GP*GP*AP*TP*GP*(XCY)P*GP*TP*GP*TP*AP*GP*GP*T)-3' (chains D, F)
GTGGATGCGTGTAGGT

Sequence of entity 2 (E, G), FASTA

>1YFH_2 5'-D(*CP*CP*TP*AP*CP*AP*CP*AP*CP*AP*TP*CP*CP*AP*CP*A)-3' (chains E, G)
CCTACACACATCCACA

Sequence of entity 3 (A, B, C), FASTA

>1YFH_3 Methylated-DNA--protein-cysteine methyltransferase (chains A, B, C)
MDKDCEMKRTTLDSPLGKLELSGCEQGLHEIKLLGKGTSAADAVEVPAPAAVLGGPEPLM
QCTAWLNAYFHQPEAIEEFPVPALHHPVFQQESFTRQVLWKLLKVVKFGEVISYQQLAAL
AGNPKAARAVGGAMRGNPVPILIPCHRVVCSSGAVGNYSGGLAVKEWLLAHEGHRLGKP

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3

Primary citation

The structure of the human AGT protein bound to DNA and its implications for damage detection. Duguid, E.M., Rice, P.A., He, C. J Mol Biol (2005) 350:657-666. DOI 10.1016/j.jmb.2005.05.028 · PubMed

Other PDB entries of the same protein (UniProt P16455 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1QNT 1.9 Å, X-ray structure of human O6alkylguanine-DNA alkyltransferase
1EH6 2.0 Å, Human O6-alkylguanine-DNA alkyltransferase
1EH7 2.0 Å, Methylated human O6-alkylguanine-DNA alkyltransferase
9QF2 2.42 Å, Cryo-EM structure of the fully Coronin-1B-decorated actin filament in the ADP state.
1EH8 2.5 Å, Benzylated human O6-alkylguanine-DNA alkyltransferase
28OP 2.7 Å, Structure of the human inner kinetochore CCAN and CENP-C bound to DNA
9QEY 2.74 Å, Cryo-EM structure of the actin filament bound by a single Coronin-1B molecule.
9QFB 2.74 Å, Cryo-EM structure of the fully Coronin-1B-decorated actin filament in the ADP state.
9QFQ 2.76 Å, Cryo-EM structure of the cofilactin barbed end bound by AIP1
9DI0 3.1 Å, Cryo-EM structure of Kif18A bound to a microtubule
9QFE 3.12 Å, Cryo-EM structure of the actin filament hetero-decorated by Coronin-1 and Cofilin-1 on…
9QFW 3.16 Å, Cryo-EM structure of the cofilactin barbed end bound by two AIP1 molecules

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