MolNFT v1 · #153380 · protein

Crystal structure of ligand-free RV0187.

6JCM · Probable O-methyltransferase: “Crystal structure of ligand-free RV0187.”. X-ray diffraction, 8 pockets (best druggability 0.71). MolNFT v1 #153380 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6JCM
Type: protein
Length: 860 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable O-methyltransferase
UniProt: O07431
Pockets: 8 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Probable O-methyltransferase	protein	215	49% helix, 22% strand	O07431

Ligands and binding sites

ACT · Acetate ion · additive · 4 copies · chains A, B, C, D

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

Pockets

8 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	677	0.71	0.78	46	empty
2	317	0.59	0.78	43	empty
3	371	0.58	0.76	45	empty
4	148	0.48	0.78	30	empty
5	124	0.48	0.79	30	empty

Interfaces

6 interfaces between chains.

C–D · 1947 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1932 Å² buried · 20 hydrogen bonds · protein-protein
B–D · 616 Å² buried · 13 hydrogen bonds · protein-protein
A–D · 303 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 231 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6JCM · Crystal structure of ligand-free Rv0187. · the same entry in another collection · chain C against C, TM-score 1.00
O07431 · AlphaFold monomer V2.0 prediction for catechol O-methyltransferase (O07431) · 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 O07431
Elsewhere: RCSB PDB 6JCM · PDBe 6JCM · UniProt O07431

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