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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Enzyme Classification Number = 3.1.3.5

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Search Summary

This query matches 756 Structures.

Refinements

Structure Determination Methodology

experimental (756)

Scientific Name of Source Organism

	Homo sapiens (246)
	Severe acute respiratory syndrome coronavirus 2 (30)
	Escherichia coli (29)
	synthetic construct (28)
	Caldanaerobacter subterraneus subsp. tengcongensis (18)
	Xenopus laevis (18)
	Escherichia coli K-12 (14)
	Rattus norvegicus (13)
	Thermus thermophilus HB8 (11)
	Methanocaldococcus jannaschii (10)

More...

Taxonomy

	Eukaryota (346)
	Bacteria (274)
	Riboviria (81)
	Archaea (44)
	other sequences (28)
	Varidnaviria (4)
	Duplodnaviria (2)
	unclassified sequences (1)

Experimental Method

	X-RAY DIFFRACTION (686)
	ELECTRON MICROSCOPY (70)

Polymer Entity Type

	Protein (724)
	RNA (73)
	DNA (46)

Refinement Resolution (Å)

	0.5 - 1.0 (1)
	1.0 - 1.5 (62)
	1.5 - 2.0 (235)
	2.0 - 2.5 (230)
	2.5 - 3.0 (146)
	3.0 - 3.5 (57)
	3.5 - 4.0 (15)
	4.0 - 4.5 (7)
	> 4.5 (3)

Release Date

	1990 - 1994 (3)
	1995 - 1999 (12)
	2000 - 2004 (34)
	2005 - 2009 (97)
	2010 - 2014 (133)
	2015 - 2019 (215)
	2020 - 2024 (247)
	2025 - 2029 (15)

Enzyme Classification Name

	Transferases (550)
	Hydrolases (31)
	Oxidoreductases (23)
	Lyases (14)
	Isomerases (3)
	Ligases (1)

Symmetry Type

	Asymmetric (464)
	Cyclic (250)
	Dihedral (39)
	Icosahedral (4)
	Tetrahedral (3)

SCOP Classification

	Alpha and beta proteins (a/b) (165)
	Artifacts (47)
	All beta proteins (27)
	Alpha and beta proteins (a+b) (38)
	All alpha proteins (17)
	Small proteins (15)
	Membrane and cell surface proteins and peptides (5)

AllSelected

1 to 25 of 756 Structures

Page 1 of 31

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1CMA \| pdb_00001cma	Download File View File

MET REPRESSOR/DNA COMPLEX + S-ADENOSYL-METHIONINE

Somers, W.S., Phillips, S.E.V.

(1992) Nature 359: 387-393

Released	1993-10-31
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Escherichia coli
Macromolecule	PROTEIN (MET REPRESSOR) (protein) DNA (5'-D(APGPAPCPGPTPCPTPA)-3') (nucleic acid) DNA (5'-D(TPTPAPGPAPCPGPTPCP*T)-3') (nucleic acid)
Unique Ligands	SAM

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1CMC \| pdb_00001cmc	Download File View File

THREE DIMENSIONAL CRYSTAL STRUCTURES OF E. COLI MET REPRESSOR WITH AND WITHOUT COREPRESSOR

Somers, W.S., Phillips, S.E.V.

(1989) Nature 341: 705-710

Released	1993-10-31
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Escherichia coli
Macromolecule	MET REPRESSOR (protein)
Unique Ligands	MG, SAM

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1EIZ \| pdb_00001eiz	Download File View File

FTSJ RNA METHYLTRANSFERASE COMPLEXED WITH S-ADENOSYLMETHIONINE

Bugl, H., Fauman, E.B., Staker, B.L., Zheng, F., Kushner, S.R., Saper, M.A., Bardwell, J.C.A., Jakob, U.

(2000) Mol Cell 6: 349-360

Released	2000-08-30
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Escherichia coli
Macromolecule	FTSJ (protein)
Unique Ligands	SAM

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1EJ0 \| pdb_00001ej0	Download File View File

FTSJ RNA METHYLTRANSFERASE COMPLEXED WITH S-ADENOSYLMETHIONINE, MERCURY DERIVATIVE

Bugl, H., Fauman, E.B., Staker, B.L., Zheng, F., Kushner, S.R., Saper, M.A., Bardwell, J.C.A., Jakob, U.

(2000) Mol Cell 6: 349-360

Released	2000-08-30
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Escherichia coli
Macromolecule	FTSJ (protein)
Unique Ligands	HG, SAM

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1FPQ \| pdb_00001fpq	Download File View File

CRYSTAL STRUCTURE ANALYSIS OF SELENOMETHIONINE SUBSTITUTED CHALCONE O-METHYLTRANSFERASE

Zubieta, C., Dixon, R.A., Noel, J.P.

(2001) Nat Struct Biol 8: 271-279

Released	2001-03-07
Method	X-RAY DIFFRACTION 2 Å
Organisms	Medicago sativa
Macromolecule	ISOLIQUIRITIGENIN 2'-O-METHYLTRANSFERASE (protein)
Unique Ligands	SAM

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1G60 \| pdb_00001g60	Download File View File

Crystal Structure of Methyltransferase MboIIa (Moraxella bovis)

Osipiuk, J., Walsh, M.A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

(2003) Nucleic Acids Res 31: 5440-5448

Released	2002-05-01
Method	X-RAY DIFFRACTION 1.74 Å
Organisms	Moraxella bovis
Macromolecule	Adenine-specific Methyltransferase MboIIA (protein)
Unique Ligands	NA, SAM

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1H1D \| pdb_00001h1d	Download File View File

Catechol O-Methyltransferase

Archer, M., Rodrigues, M.L., Matias, P.M., Bonifacio, M.J., Learmonth, D.A., Soares-da-Silva, P., Carrondo, M.A.

(2002) Mol Pharmacol 62: 795

Released	2003-07-17
Method	X-RAY DIFFRACTION 2 Å
Organisms	Rattus norvegicus
Macromolecule	CATECHOL-O-METHYLTRANSFERASE (protein)
Unique Ligands	BIA, MG, SAM

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1HMY \| pdb_00001hmy	Download File View File

CRYSTAL STRUCTURE OF THE HHAI DNA METHYLTRANSFERASE COMPLEXED WITH S-ADENOSYL-L-METHIONINE

Cheng, X.

(1993) Cell 74: 299-307

Released	1993-10-31
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Haemophilus haemolyticus
Macromolecule	HaeIII METHYLTRANSFERASE (protein)
Unique Ligands	SAM

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1I9G \| pdb_00001i9g	Download File View File

CRYSTAL STRUCTURE OF AN ADOMET DEPENDENT METHYLTRANSFERASE

Gupta, A., Kumar, P.H., Dineshkumar, T.K., Varshney, U., Subramanya, H.S., TB Structural Genomics Consortium (TBSGC)

(2001) J Mol Biology 312: 381-391

Released	2001-09-26
Method	X-RAY DIFFRACTION 1.98 Å
Organisms	Mycobacterium tuberculosis
Macromolecule	HYPOTHETICAL PROTEIN RV2118C (protein)
Unique Ligands	SAM

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1JG4 \| pdb_00001jg4	Download File View File

Crystal Structure of L-isoaspartyl (D-aspartyl) O-methyltransferase with S-adenosylmethionine

Griffith, S.C., Sawaya, M.R., Boutz, D., Thapar, N., Katz, J., Clarke, S., Yeates, T.O.

(2001) J Mol Biology 313: 1103-1116

Released	2001-11-16
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Pyrococcus furiosus
Macromolecule	protein-L-isoaspartate O-methyltransferase (protein)
Unique Ligands	SAM

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1KIA \| pdb_00001kia	Download File View File

Crystal structure of glycine N-methyltransferase complexed with S-adenosylmethionine and acetate

Takusagawa, F., Huang, Y.

To be published

Released	2003-06-10
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Rattus norvegicus
Macromolecule	Glycine N-methyltransferase (protein)
Unique Ligands	ACT, SAM

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1MJ2 \| pdb_00001mj2	Download File View File

METHIONINE REPRESSOR MUTANT (Q44K) PLUS COREPRESSOR (S-ADENOSYL METHIONINE) COMPLEXED TO A CONSENSUS OPERATOR SEQUENCE

Garvie, C.W., Phillips, S.E.V.

(2000) Structure 8: 905-914

Released	1999-08-02
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Escherichia coli
Macromolecule	PROTEIN (METHIONINE REPRESSOR) (protein) DNA (5'-D(TPTPAPGPAPCPGPTPCPTPAPGPAPCPGPTPCPTP*A)-3') (nucleic acid)
Unique Ligands	CA, SAM

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1MJL \| pdb_00001mjl	Download File View File

METHIONINE REPRESSOR MUTANT (Q44K) COMPLEX WITH THE COREPRESSOR SAM (S-ADENOSYL METHIONINE) FROM ESCHERICHIA COLI

Garvie, C.W., Phillips, S.E.V.

(1997) Thesis

Released	1998-04-29
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Escherichia coli
Macromolecule	METHIONINE REPRESSOR PROTEIN METJ (protein)
Unique Ligands	SAM

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1MJO \| pdb_00001mjo	Download File View File

METHIONINE HOLOREPRESSOR MUTANT (Q44K) PLUS COREPRESSOR (S-ADENOSYL METHIONINE) COMPLEXED TO THE MINIMAL MET CONSENSUS OPERATOR WITH THE CENTRAL TA STEP MUTATED TO AT

Garvie, C.W., Phillips, S.E.V.

(2000) Structure 8: 905-914

Released	1999-08-02
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Escherichia coli
Macromolecule	METHIONINE REPRESSOR (protein) CONSENSUS DNA OPERATOR DUPLEX WITH THE CENTRAL TA STEP MUTATED TO AT (nucleic acid)
Unique Ligands	CA, SAM

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1MJQ \| pdb_00001mjq	Download File View File

METHIONINE REPRESSOR MUTANT (Q44K) PLUS COREPRESSOR (S-ADENOSYL METHIONINE) COMPLEXED TO AN ALTERED MET CONSENSUS OPERATOR SEQUENCE

Garvie, C.W., Phillips, S.E.V.

(2000) Structure 8: 905-914

Released	1999-08-02
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Escherichia coli
Macromolecule	METHIONINE REPRESSOR (protein) MUTATED MET CONSENSUS OPERATOR DUPLEX (nucleic acid)
Unique Ligands	SAM

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1MSK \| pdb_00001msk	Download File View File

METHIONINE SYNTHASE (ACTIVATION DOMAIN)

Dixon, M.M., Huang, S., Matthews, R.G., Ludwig, M.L.

(1996) Structure 4: 1263-1275

Released	1997-04-01
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Escherichia coli K-12
Macromolecule	COBALAMIN-DEPENDENT METHIONINE SYNTHASE (protein)
Unique Ligands	ACT, SAM

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1N2X \| pdb_00001n2x	Download File View File

Crystal Structure Analysis of TM0872, a Putative SAM-dependent Methyltransferase, Complexed with SAM

Miller, D.J., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

(2003) Protein Sci 12: 1432-1442

Released	2003-01-28
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Thermotoga maritima
Macromolecule	S-adenosyl-methyltransferase mraW (protein)
Unique Ligands	SAM, SO4

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1N6A \| pdb_00001n6a	Download File View File

Structure of SET7/9

Kwon, T.W., Chang, J.H., Kwak, E., Lee, C.W., Joachimiak, A., Kim, Y.C., Lee, J., Cho, Y.

(2003) EMBO J 22: 292-303

Released	2003-02-04
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Homo sapiens
Macromolecule	SET domain-containing protein 7 (protein)
Unique Ligands	SAM

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1N6C \| pdb_00001n6c	Download File View File

Structure of SET7/9

Kwon, T.W., Chang, J.H., Cho, Y.

(2003) EMBO J 22: 292-303

Released	2003-02-04
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	SET domain-containing protein 7 (protein)
Unique Ligands	SAM

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1NBH \| pdb_00001nbh	Download File View File

Structure of glycine N-methyltransferase complexed with S-adenosylmethionine and acetate, GNMT:SAM:Ace

Takata, Y., Takusagawa, F.

(2003) Biochemistry 42: 8394-8402

Released	2003-03-04
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Rattus norvegicus
Macromolecule	Glycine N-methyltransferase (protein)
Unique Ligands	ACT, SAM

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1NBI \| pdb_00001nbi	Download File View File

Structure of R175K mutated glycine N-methyltransferase complexed with S-adenosylmethionine, R175K:SAM.

Takata, Y., Takusagawa, F.

(2003) Biochemistry 42: 8394-8402

Released	2003-03-04
Method	X-RAY DIFFRACTION 3 Å
Organisms	Rattus norvegicus
Macromolecule	Glycine N-methyltransferase (protein)
Unique Ligands	SAM

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1NT2 \| pdb_00001nt2	Download File View File

CRYSTAL STRUCTURE OF FIBRILLARIN/NOP5P COMPLEX

Aittaleb, M., Rashid, R., Chen, Q., Palmer, J.R., Daniels, C.J., Li, H.

(2003) Nat Struct Biol 10: 256-263

Released	2003-04-01
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Archaeoglobus fulgidus DSM 4304
Macromolecule	Fibrillarin-like pre-rRNA processing protein (protein) conserved hypothetical protein (protein)
Unique Ligands	SAM

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1NV8 \| pdb_00001nv8	Download File View File

N5-glutamine methyltransferase, HemK

Schubert, H.L., Phillips, J.D., Hill, C.P.

(2003) Biochemistry 42: 5592-5599

Released	2003-05-27
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Thermotoga maritima
Macromolecule	hemK protein (protein)
Unique Ligands	MEQ, SAM

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1NW3 \| pdb_00001nw3	Download File View File

Structure of the Catalytic domain of human DOT1L, a non-SET domain nucleosomal histone methyltransferase

Min, J.R., Feng, Q., Li, Z.H., Zhang, Y., Xu, R.M.

(2003) Cell 112: 711-723

Released	2003-03-25
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	histone methyltransferase DOT1L (protein)
Unique Ligands	ACT, SAM, SO4

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1NW5 \| pdb_00001nw5	Download File View File

Structure of the beta class N6-adenine DNA methyltransferase RsrI bound to S-ADENOSYLMETHIONINE

Thomas, C.B., Scavetta, R.D., Gumport, R.I., Churchill, M.E.A.

(2003) J Biological Chem 278: 26094-26101

Released	2003-07-29
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Cereibacter sphaeroides
Macromolecule	MODIFICATION METHYLASE RSRI (protein)
Unique Ligands	CL, SAM

1 to 25 of 756 Structures

Page 1 of 31

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

SCOP Classification

1CMA | pdb_00001cma

1CMC | pdb_00001cmc

1EIZ | pdb_00001eiz

1EJ0 | pdb_00001ej0

1FPQ | pdb_00001fpq

1G60 | pdb_00001g60

1H1D | pdb_00001h1d

1HMY | pdb_00001hmy

1I9G | pdb_00001i9g

1JG4 | pdb_00001jg4

1KIA | pdb_00001kia

1MJ2 | pdb_00001mj2

1MJL | pdb_00001mjl

1MJO | pdb_00001mjo

1MJQ | pdb_00001mjq

1MSK | pdb_00001msk

1N2X | pdb_00001n2x

1N6A | pdb_00001n6a

1N6C | pdb_00001n6c

1NBH | pdb_00001nbh

1NBI | pdb_00001nbi

1NT2 | pdb_00001nt2

1NV8 | pdb_00001nv8

1NW3 | pdb_00001nw3

1NW5 | pdb_00001nw5