7K3D: NTMT1

The structure of NTMT1 in complex with compound DC1-13. Determined by X-ray diffraction at 2.34 Å resolution. Released 14 Apr 2021.

Method: X-ray diffraction
Resolution: 2.34 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,876
Mol. weight: 56.54 kDa
Ligands: VWP, SAH
Released: 14 Apr 2021

Explore 7K3D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7K3D contains 31 α-helices and 18 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: 15 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	9-21	13
α-helix	27-30	4
α-helix	35-37	3
α-helix	38-54	17
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	94-104	11
α-helix	107-110	4
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	143-156	14
β-strand	157-170	14	1
β-strand	174-177	4	1
β-strand	182-186	5	1
α-helix	187-196	10
β-strand	201-206	6	1
α-helix	215	1
β-strand	216-222	7	1

Chain B: 16 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	9-21	13
α-helix	27-30	4
α-helix	35-37	3
α-helix	38-54	17
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	107-110	4
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	157-170	14	1
β-strand	174-177	4	1
β-strand	182-186	5	1
α-helix	187-196	10
α-helix	199-200	2
β-strand	201-206	6	1
α-helix	215	1
β-strand	216-222	7	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
N-terminal Xaa-Pro-Lys N-methyltransferase 1	A, B	protein	241	Homo sapiens	Q9BV86 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7K3D_1 N-terminal Xaa-Pro-Lys N-methyltransferase 1 (chains A, B)
MGSSHHHHHHSSGLVPRGSTSEVIEDEKQFYSKAKTYWKQIPPTVDGMLGGYGHISSIDI
NSSRKFLQRFLREGPNKTGTSCALDCGAGIGRITKRLLLPLFREVDMVDITEDFLVQAKT
YLGEEGKRVRNYFCCGLQDFTPEPDSYDVIWIQWVIGHLTDQHLAEFLRRCKGSLRPNGI
IVIKDNMAQEGVILDDVDSSVCRDLDVVRRIICSAGLSLLAEERQENLPDEIYHVYSFAL
R

Ligands and cofactors

ID	Name	Formula	Copies
VWP	N~2~-{(2S)-1-[(naphthalen-1-yl)acetyl]-2,5-dihydro-1H-pyrrole-2-carbonyl}-L-lys…	C29 H40 N8 O4	2
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	2

Primary citation

Structure-based Discovery of Cell-Potent Peptidomimetic Inhibitors for Protein N-Terminal Methyltransferase 1. Chen, D., Dong, G., Deng, Y. et al. ACS Med Chem Lett (2021) 12:485-493. DOI 10.1021/acsmedchemlett.1c00012 · 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
6WJ7 1.42 Å, The structure of NTMT1 in complex with compound C2A
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

Browse structure collections

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