PDB-9fkv: compound 2c bound KMT9 crystal structure

ID or keywords:

Entry

Database: PDB / ID: 9fkv

Title

compound 2c bound KMT9 crystal structure

Components

Methyltransferase N6AMT1
Multifunctional methyltransferase subunit TRM112-like protein

Keywords

TRANSFERASE / Protein transferase / gene regulation

Function / homology

Function and homology information

arsonoacetate metabolic process / arsenite methyltransferase activity / protein-glutamine N-methyltransferase activity / eRF1 methyltransferase complex / peptidyl-glutamine methylation / tRNA (m2G10) methyltransferase complex / rRNA (guanine-N7)-methylation / tRNA methyltransferase activator activity / toxin metabolic process / site-specific DNA-methyltransferase (adenine-specific) activity ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.47 Å

Authors

Sheng, W. / Eric, M. / Roland, S.

Funding support

Germany, 4items

Organization	Grant number	Country
German Research Foundation (DFG)	SFB992	Germany
German Research Foundation (DFG)	Schu688	Germany
German Research Foundation (DFG)	EXC-2189	Germany
German Research Foundation (DFG)	DKTK FR01-374	Germany

Citation

Journal: To Be Published
Title: compound 2c bound KMT9 crystal structure
Authors: Sheng, W. / Eric, M. / Roland, S.

History

Deposition	Jun 4, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 18, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9fkv.cif.gz	340.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9fkv.ent.gz		Display	PDB format
PDBx/mmJSON format	9fkv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fk/9fkv ftp://data.pdbj.org/pub/pdb/validation_reports/fk/9fkv	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#60 - Dec 2004 Ubiquitin similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1)

Deposited unit

A: Methyltransferase N6AMT1

B: Multifunctional methyltransferase subunit TRM112-like protein

hetero molecules

36.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	110.346, 110.346, 130.690
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	178
Space group name H-M	P6₁22

#1: Protein	Methyltransferase N6AMT1 / HemK methyltransferase family member 2 / M.HsaHemK2P / Lysine N-methyltransferase 9 / ...HemK methyltransferase family member 2 / M.HsaHemK2P / Lysine N-methyltransferase 9 / Methylarsonite methyltransferase N6AMT1 / Protein N(5)-glutamine methyltransferase Mass: 21804.064 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: N6AMT1, C21orf127, HEMK2, KMT9, PRED28 / Production host: Escherichia coli (E. coli) References: UniProt: Q9Y5N5, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Protein	Multifunctional methyltransferase subunit TRM112-like protein / tRNA methyltransferase 112 homolog Mass: 14272.412 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRMT112, AD-001, HSPC152, HSPC170 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UI30
#3: Chemical	ChemComp-A1IC8 / (2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[(3~{R})-3-azanylbutyl]amino]-2-azanyl-butanoic acid Mass: 438.481 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₈H₃₀N₈O₅ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.18 Å³/Da / Density % sol: 61.36 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 52% Tacsimate, PH 7.7

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 11, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.47→47.78 Å / Num. obs: 80265 / % possible obs: 99.9 % / Redundancy: 39.4 % / CC_1/2: 1 / R_merge(I) obs: 0.065 / Net I/σ(I): 34.6
Reflection shell	Resolution: 1.47→1.49 Å / Num. unique obs: 3836 / CC_1/2: 0.563

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
PDB_EXTRACT	3.27	data extraction
MOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.47→47.78 Å / Cor.coef. F_o:F_c: 0.974 / Cor.coef. F_o:F_c free: 0.965 / SU B: 2.137 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.053
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1904	4000	4.988 %	RANDOM
R_work	0.1584	76199	-	-
all	0.16	-	-	-
obs	-	80199	99.873 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 26.316 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.537 Å²	-0.269 Å²	-0 Å²
2-	-	-0.537 Å²	0 Å²
3-	-	-	1.742 Å²

Refinement step

Cycle: LAST / Resolution: 1.47→47.78 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2413	0	31	137	2581

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.012	2563
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2427
X-RAY DIFFRACTION	r_angle_refined_deg	1.732	1.645	3494
X-RAY DIFFRACTION	r_angle_other_deg	0.6	1.552	5675
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.742	5	328
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.324	5	18
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.838	10	441
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	17.448	10	105
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	406
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	2898
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	473
X-RAY DIFFRACTION	r_nbd_refined	0.255	0.2	418
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.193	0.2	2180
X-RAY DIFFRACTION	r_nbtor_refined	0.169	0.2	1223
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	1327
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.149	0.2	98
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.186	0.2	16
X-RAY DIFFRACTION	r_nbd_other	0.227	0.2	66
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.244	0.2	18
X-RAY DIFFRACTION	r_mcbond_it	5.503	2.386	1277
X-RAY DIFFRACTION	r_mcbond_other	5.501	2.386	1277
X-RAY DIFFRACTION	r_mcangle_it	5.836	3.587	1598
X-RAY DIFFRACTION	r_mcangle_other	5.834	3.59	1599
X-RAY DIFFRACTION	r_scbond_it	9.169	3.003	1286
X-RAY DIFFRACTION	r_scbond_other	9.166	3.005	1287
X-RAY DIFFRACTION	r_scangle_it	9.028	4.252	1889
X-RAY DIFFRACTION	r_scangle_other	9.026	4.255	1890
X-RAY DIFFRACTION	r_lrange_it	8.207	33.725	2688
X-RAY DIFFRACTION	r_lrange_other	8.233	33.275	2662
X-RAY DIFFRACTION	r_rigid_bond_restr	11.101	3	4990

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.47-1.506	0.32	294	0.305	5461	X-RAY DIFFRACTION	98.5952
1.506-1.547	0.293	308	0.25	5380	X-RAY DIFFRACTION	100
1.547-1.592	0.231	267	0.201	5278	X-RAY DIFFRACTION	100
1.592-1.641	0.221	265	0.166	5136	X-RAY DIFFRACTION	100
1.641-1.695	0.189	267	0.143	4961	X-RAY DIFFRACTION	100
1.695-1.754	0.182	259	0.132	4791	X-RAY DIFFRACTION	100
1.754-1.82	0.191	217	0.121	4695	X-RAY DIFFRACTION	100
1.82-1.894	0.161	241	0.119	4477	X-RAY DIFFRACTION	100
1.894-1.978	0.179	232	0.132	4283	X-RAY DIFFRACTION	100
1.978-2.075	0.176	217	0.141	4126	X-RAY DIFFRACTION	100
2.075-2.187	0.165	186	0.141	3961	X-RAY DIFFRACTION	100
2.187-2.319	0.18	204	0.146	3721	X-RAY DIFFRACTION	100
2.319-2.479	0.183	190	0.148	3521	X-RAY DIFFRACTION	100
2.479-2.677	0.186	176	0.152	3282	X-RAY DIFFRACTION	100
2.677-2.931	0.198	156	0.16	3050	X-RAY DIFFRACTION	100
2.931-3.276	0.172	154	0.174	2754	X-RAY DIFFRACTION	100
3.276-3.78	0.179	115	0.157	2485	X-RAY DIFFRACTION	100
3.78-4.622	0.185	105	0.135	2138	X-RAY DIFFRACTION	100
4.622-6.506	0.219	88	0.191	1680	X-RAY DIFFRACTION	100
6.506-47.78	0.214	59	0.213	1019	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.003	0.0032	0.004	0.0125	0.0005	0.0069	-0.0008	0.0005	0.0002	-0.002	0.0008	0.001	-0.0004	0.0008	-0	0.0118	0	0	0.0116	0.0001	0.0001	-42.4812	-6.8776	-16.5199
2	0.0297	0.0062	0.0106	0.0161	0.0215	0.0303	-0.0005	0.0028	0.002	-0.0012	0.0015	-0.0011	-0.0013	-0.0018	-0.001	0.0116	-0	-0	0.012	0.0002	0.0006	-47.1325	-26.8473	-2.5235

Refinement TLS group

Selection: ALL

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