6KDR: Human NRMT2

Crystal structure of human NRMT2 in complex with human centromere protein B peptide. Determined by X-ray diffraction at 2.11 Å resolution. Released 8 Jul 2020.

Method: X-ray diffraction
Resolution: 2.11 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,935
Mol. weight: 58.4 kDa
Ligands: SAH
Released: 8 Jul 2020

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

Secondary structure: helices and β-sheets

6KDR contains 30 α-helices and 32 β-strands across 4 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, 15 β-strands

Element	Residues	Length	Sheet
β-strand	61-63	3	1
α-helix	65-77	13
α-helix	83-86	4
α-helix	91-93	3
α-helix	94-108	15
β-strand	109	1	2
β-strand	115	1	2
β-strand	119-123	5	3
α-helix	129-130	2
α-helix	131-135	5
β-strand	141-146	6	3
α-helix	149-158	10
α-helix	160-165	6
β-strand	166-171	6	3
α-helix	174-176	3
α-helix	179-180	2
β-strand	184-190	7	3
α-helix	193-195	3
α-helix	198-210	13
β-strand	212-223	12	3
β-strand	225	1	4
β-strand	229-232	4	5
β-strand	237-239	3	5
β-strand	241	1	4
α-helix	242-251	10
β-strand	256-261	6	3
α-helix	262-263	2
β-strand	269	1	6
α-helix	270-271	2
β-strand	272-277	6	3

Chain B: 14 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	60-63	4	5
α-helix	65-76	12
α-helix	83-86	4
α-helix	91-93	3
α-helix	94-106	13
β-strand	109	1	7
β-strand	115	1	7
β-strand	119-123	5	8
α-helix	129-130	2
α-helix	131-135	5
β-strand	141-145	5	8
α-helix	149-158	10
α-helix	163-165	3
β-strand	166-170	5	8
α-helix	174-176	3
α-helix	179-180	2
β-strand	184-190	7	8
α-helix	193-195	3
α-helix	198-211	14
β-strand	212-223	12	8
β-strand	225	1	9
β-strand	230-232	3	1
β-strand	237-239	3	1
β-strand	241	1	9
α-helix	242-251	10
β-strand	256-261	6	8
α-helix	262-263	2
β-strand	269	1	10
β-strand	272-277	6	8

Chain D: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	4	1	6

Chain E: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	4	1	10
α-helix	5-7	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Alpha N-terminal protein methyltransferase 1B	A, B	protein	244	Homo sapiens	Q5VVY1 (AlphaFold model)
Peptide from Major centromere autoantigen B	D, E	protein	9	Homo sapiens	P07199 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6KDR_1 Alpha N-terminal protein methyltransferase 1B (chains A, B)
MGSSHHHHHHSSGLVPRGSHMVINGEMQFYARAKLFYQEVPATEEGMMGNFIELSSPDIQ
ASQKFLRKFVGGPGRAGTDCALDCGSGIGRVSKHVLLPVFNSVELVDMMESFLLEAQNYL
QVKGDKVESYHCYSLQEFTPPFRRYDVIWIQWVSGHLTDKDLLAFLSRCRDGLKENGIII
LKDNVAREGCILDLSDSSVTRDMDILRSLIRKSGLVVLGQEKQDGFPEQCIPVWMFALHS
DRHS

Sequence of entity 2 (D, E), FASTA

>6KDR_2 Peptide from Major centromere autoantigen B (chains D, E)
GPKRRQLTF

Ligands and cofactors

ID	Name	Formula	Copies
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	2

Water and common crystallization additives (GOL, CL) are not listed.

Primary citation

Substrate-enzyme engagement regulates state-specific alpha-N methylation of NRMT2. Wu, R., Yue, Y., Zheng, X. et al. To be published.

Other PDB entries of the same protein (UniProt Q5VVY1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6DUB 1.2 Å, Crystal structure of a methyltransferase
6KDS 1.84 Å, Crystal structure of human NRMT2 in complex with alpha-N-monomethylated human CENP-A…
5UBB 2.0 Å, Crystal structure of human alpha N-terminal protein methyltransferase 1B

Browse structure collections

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