6WJ7: NTMT1

Name: PDB 6WJ7: The structure of NTMT1 in complex with compound C2A
Published: 2020-08-19
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

The structure of NTMT1 in complex with compound C2A. Determined by X-ray diffraction at 1.42 Å resolution. Released 19 Aug 2020.

Method: X-ray diffraction
Resolution: 1.42 Å
Organisms: Homo sapiens, synthetic construct
Chains: 2
Atoms: 2,049
Mol. weight: 28.36 kDa
Ligands: AN6
Released: 19 Aug 2020

Explore 6WJ7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6WJ7 contains 16 α-helices and 13 β-strands across 2 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: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	5	1	4

Chain B: 16 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	9-21	13
α-helix	27-30	4
α-helix	35-37	3
α-helix	38-53	16
α-helix	59-61	3
β-strand	64-68	5	1
α-helix	74-75	2
α-helix	76-80	5
β-strand	86-91	6	1
α-helix	94-103	10
α-helix	105-110	6
β-strand	111-116	6	1
α-helix	119-121	3
α-helix	124-125	2
β-strand	129-135	7	1
α-helix	138-140	3
α-helix	143-155	13
β-strand	157-168	12	1
β-strand	170	1	2
β-strand	174-177	4	3
β-strand	182-185	4	3
β-strand	186	1	2
α-helix	187-196	10
α-helix	199-200	2
β-strand	201-206	6	1
α-helix	207-208	2
β-strand	214	1	4
β-strand	217-222	6	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
N-terminal Xaa-Pro-Lys N-methyltransferase 1	B	protein	241	Homo sapiens	Q9BV86 (AlphaFold model)
Gly-pro-lys-arg-ile-ala-NH2	A	protein	7	synthetic construct

Sequence of entity 1 (B), FASTA

>6WJ7_1 N-terminal Xaa-Pro-Lys N-methyltransferase 1 (chains B)
MGSSHHHHHHSSGLVPRGSTSEVIEDEKQFYSKAKTYWKQIPPTVDGMLGGYGHISSIDI
NSSRKFLQRFLREGPNKTGTSCALDCGAGIGRITKRLLLPLFREVDMVDITEDFLVQAKT
YLGEEGKRVRNYFCCGLQDFTPEPDSYDVIWIQWVIGHLTDQHLAEFLRRCKGSLRPNGI
IVIKDNMAQEGVILDDVDSSVCRDLDVVRRIICSAGLSLLAEERQENLPDEIYHVYSFAL
R

Sequence of entity 2 (A), FASTA

>6WJ7_2 GLY-PRO-LYS-ARG-ILE-ALA-NH2 (chains A)
GPKRIAX

Ligands and cofactors

ID	Name	Formula	Copies
AN6	5'-{[(3S)-3-amino-3-carboxypropyl](ethyl)amino}-5'-deoxyadenosine	C16 H25 N7 O5	1

Primary citation

Probing the Plasticity in the Active Site of Protein N-terminal Methyltransferase 1 Using Bisubstrate Analogues. Chen, D., Dong, C., Dong, G. et al. J Med Chem (2020) 63:8419-8431. DOI 10.1021/acs.jmedchem.0c00770 · PubMed

Other PDB entries of the same protein (UniProt Q9BV86 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5CVD 1.3 Å, Crystal structure of human NRMT1 in complex with alpha-N-dimethylated human CENP-A peptide
5E1D 1.45 Å, NTMT1 in complex with YPKRIA peptide
6DTN 1.48 Å, The structure of NTMT1 in complex with compound DC100-1
6KDQ 1.5 Å, Crystal structure of human NRMT1 in complex with alpha-N-monomethylated human CENP-A…
5CVE 1.5 Å, Crystal Structure of human NRMT1 in complex with dimethylated fly H2B peptide and SAH
6PVB 1.5 Å, The structure of NTMT1 in complex with compound 6
5E1B 1.65 Å, Crystal structure of NRMT1 in complex with SPKRIA peptide
6WH8 1.73 Å, The structure of NTMT1 in complex with compound BM-30
2EX4 1.75 Å, Crystal Structure of Human methyltransferase AD-003 in complex with…
5E1M 1.75 Å, Crystal structure of NTMT1 in complex with PPKRIA peptide
5E2A 1.75 Å, Crystal structure of NTMT1 in complex with N-terminally methylated SPKRIA peptide
6PVA 1.84 Å, The structure of NTMT1 in complex with compound 11

Browse structure collections

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