MolNFT v1 · #117219 · protein

Crystal structure of NTMT1 in complex with ppkria peptide

5E1M · N-terminal xaa-pro-lys N-methyltransferase 1: “Crystal structure of NTMT1 in complex with ppkria peptide”. X-ray diffraction, 2 ligands (SAH, UNX), 6 pockets (best druggability 0.80). MolNFT v1 #117219 on GenesisL1: 3D structure…

PDB: 5E1M
Type: protein
Length: 465 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: N-terminal xaa-pro-lys N-methyltransferase 1; RCC1
EC: 2.1.1.244
UniProt: Q9BV86
Ligands: SAH, UNX
Pockets: 6 · best druggability 0.80

Structure

x-ray diffraction · 3 distinct chains · 40% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	N-terminal xaa-pro-lys N-methyltransferase 1 (EC 2.1.1.244)	protein	227	40% helix, 27% strand	Q9BV86
B	N-terminal xaa-pro-lys N-methyltransferase 1 (EC 2.1.1.244)	protein	226	42% helix, 26% strand	Q9BV86
D, E	RCC1	protein	6	0% helix, 17% strand	—

Ligands and binding sites

SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
UNX · Unknown atom or ion · ion · 43 copies · chains A, B, E, D
GOL · Glycerol · additive · 3 copies · chains A, D, B, E

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	149	0.80	0.96	28	SAH, UNX
2	143	0.78	0.95	29	SAH, UNX
3	332	0.68	0.82	44	UNX, GOL
4	65	0.50	0.86	24	GOL
5	120	0.43	0.77	28	UNX

Interfaces

4 interfaces between chains.

A–B · 509 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 507 Å² buried · 8 hydrogen bonds · protein-protein
B–E · 500 Å² buried · 7 hydrogen bonds · protein-protein
A–E · 29 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5E1M · Crystal structure of NTMT1 in complex with PPKRIA peptide · the same entry in another collection · chain A against A, TM-score 1.00
Q9BV86 · AlphaFold monomer V2.0 prediction for N-terminal xaa-pro-lys N-methyltransferase 1… · a predicted model of the same protein · chain B against A, TM-score 0.98

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q9BV86
Elsewhere: RCSB PDB 5E1M · PDBe 5E1M · UniProt Q9BV86

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