MolNFT v1 · #116775 · protein

The structure of PKMT1 from rickettsia prowazekii

5DO0 · Protein lysine methyltransferase 1: “The structure of PKMT1 from rickettsia prowazekii”. X-ray diffraction, 17 pockets (best druggability 0.66). MolNFT v1 #116775 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5DO0
Type: protein
Length: 1,016 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein lysine methyltransferase 1
UniProt: O05979
Pockets: 17 · best druggability 0.66

Structure

x-ray diffraction · 2 distinct chains · 46% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Protein lysine methyltransferase 1	protein	511	48% helix, 15% strand	O05979
A	Protein lysine methyltransferase 1	protein	505	44% helix, 15% strand	O05979

Pockets

17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	452	0.66	0.78	50	empty
2	605	0.66	0.76	50	empty
3	208	0.64	0.83	25	empty
4	301	0.60	0.78	38	empty
5	484	0.60	0.75	45	empty

Interfaces

1 interface between chains.

B–A · 1555 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

5DO0 · The structure of PKMT1 from Rickettsia prowazekii · the same entry in another collection · chain B against B, TM-score 1.00
O05979 · AlphaFold monomer V2.0 prediction for uncharacterized protein RP789 (O05979) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 O05979
Elsewhere: RCSB PDB 5DO0 · PDBe 5DO0 · UniProt O05979

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