MolNFT v1 · #46656 · protein

PPM1 in the absence of 1,8-ans (cf 1JD)

2OB2 · Leucine carboxyl methyltransferase 1: “PPM1 in the absence of 1,8-ans (cf 1JD)”. X-ray diffraction, 2 ligands (SAH, PO4), 14 pockets (best druggability 0.82). MolNFT v1 #46656 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 2OB2
Type: protein
Length: 981 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Leucine carboxyl methyltransferase 1
EC: 2.1.1.-
UniProt: Q04081
Ligands: SAH, PO4
Pockets: 14 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 53% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Leucine carboxyl methyltransferase 1 (EC 2.1.1.-)	protein	327	53% helix, 15% strand	Q04081

Ligands and binding sites

SAH · S-adenosyl-L-homocysteine · ligand · 3 copies · chains A, B, C
PO4 · Phosphate ion · ion · chains A
GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	893	0.82	0.84	72	empty
2	490	0.76	0.84	54	SAH
3	466	0.75	0.84	56	SAH, GOL
4	483	0.74	0.82	55	SAH
5	325	0.72	0.85	63	GOL

Interfaces

2 interfaces between chains.

A–C · 979 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 668 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 modified (methylation).

Compared structures

2OB2 · ppm1 in the absence of 1,8-ANS (cf 1JD) · the same entry in another collection · chain A against A, TM-score 1.00
Q04081 · AlphaFold monomer V2.0 prediction for leucine carboxyl methyltransferase 1 (Q04081) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q04081
Elsewhere: RCSB PDB 2OB2 · PDBe 2OB2 · UniProt Q04081

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