MolNFT v1 · #154519 · protein

Crystal structure of human NRMT2 in complex with human centromere protein B peptide

6KDR · Alpha N-terminal protein methyltransferase 1B: “Crystal structure of human NRMT2 in complex with human centromere protein B peptide”. X-ray diffraction, 2 ligands (SAH, CL), 5 pockets (best druggability 0.78). MolNFT v1 #154519 on…

PDB: 6KDR
Type: protein
Length: 455 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alpha N-terminal protein methyltransferase 1B; Peptide from major centromere autoantigen B
EC: 2.1.1.299
UniProt: Q5VVY1, P07199
Ligands: SAH, CL
Pockets: 5 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 37% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Alpha N-terminal protein methyltransferase 1B (EC 2.1.1.299)	protein	220	40% helix, 29% strand	Q5VVY1
D	Peptide from major centromere autoantigen B	protein	6	0% helix, 17% strand	P07199
E	Peptide from major centromere autoantigen B	protein	9	0% helix, 11% strand	P07199

Ligands and binding sites

SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
CL · Chloride ion · ion · 3 copies · chains A, B, E
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

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	243	0.78	0.91	49	SAH, GOL
2	263	0.78	0.90	49	SAH, GOL
3	231	0.55	0.77	31	empty
4	59	0.48	0.85	16	CL
5	69	0.41	0.80	21	empty

Interfaces

5 interfaces between chains.

A–B · 799 Å² buried · 13 hydrogen bonds · protein-protein
A–D · 574 Å² buried · 11 hydrogen bonds · protein-protein
B–E · 513 Å² buried · 5 hydrogen bonds · protein-protein
A–E · 108 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 64 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6KDR · Crystal structure of human NRMT2 in complex with human centromere protein B peptide · the same entry in another collection · chain E against E, TM-score 1.00
Q5VVY1 · AlphaFold monomer V2.0 prediction for alpha N-terminal protein methyltransferase 1B… · a predicted model of the same protein · chain B against A, TM-score 0.98
P07199 · AlphaFold monomer V2.0 prediction for major centromere autoantigen B (P07199) · a predicted model of the same protein · chain D against A, TM-score 0.66

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 Q5VVY1
Every structure of UniProt P07199
Elsewhere: RCSB PDB 6KDR · PDBe 6KDR · UniProt Q5VVY1 · UniProt P07199

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