MolNFT v1 · #119999 · protein

Crystal structure of methyltransferase tled complexed with sah and teleocidin A1

5GM2 · O-methylransferase: “Crystal structure of methyltransferase tled complexed with sah and teleocidin A1”. X-ray diffraction, 2 ligands (SAH, TEX), 20 pockets (best druggability 0.88). MolNFT v1 #119999 on GenesisL1: 3D structure…

PDB: 5GM2
Type: protein
Length: 4,931 residues
Chains: 18
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: O-methylransferase
UniProt: A0A077K7L1
Ligands: SAH, TEX
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 10 distinct chains · 49% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, H	O-methylransferase	protein	281	51% helix, 17% strand	A0A077K7L1
B	O-methylransferase	protein	282	51% helix, 19% strand	A0A077K7L1
C, E, F, O, P	O-methylransferase	protein	279	50% helix, 20% strand	A0A077K7L1
G, I, Q	O-methylransferase	protein	266	49% helix, 21% strand	A0A077K7L1
J	O-methylransferase	protein	272	50% helix, 19% strand	A0A077K7L1
K	O-methylransferase	protein	267	46% helix, 16% strand	A0A077K7L1
L	O-methylransferase	protein	263	49% helix, 21% strand	A0A077K7L1
M	O-methylransferase	protein	264	49% helix, 21% strand	A0A077K7L1
N	O-methylransferase	protein	274	49% helix, 18% strand	A0A077K7L1
R	O-methylransferase	protein	273	51% helix, 11% strand	A0A077K7L1

Ligands and binding sites

SAH · S-adenosyl-L-homocysteine · ligand · 18 copies · chains A, B, C, D, E, F, G, H, I, K, J, L, M, N, O, P, Q, R
TEX · (2S,5S)-9-[(3R)-3,7-dimethylocta-1,6-dien-3-yl]-5-(hydroxymethyl)-1-methyl-2-(propan-2-yl)-1,2,4,5,6,8-hexahydro-3H-[1,4]diazonino[7,6,5-cd]indol-3-one · ligand · 18 copies · chains A, B, C, D, E, F, G, H, I, K, J, L, M, N, O, P, Q, R

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	412	0.88	0.96	61	SAH, TEX
2	420	0.88	0.95	63	SAH, TEX
3	436	0.88	0.95	60	SAH, TEX
4	410	0.87	0.95	58	SAH, TEX
5	424	0.87	0.95	62	SAH, TEX

Interfaces

49 interfaces between chains.

A–B · 4972 Å² buried · 60 hydrogen bonds · protein-protein
C–D · 4806 Å² buried · 64 hydrogen bonds · protein-protein
O–P · 4738 Å² buried · 58 hydrogen bonds · protein-protein
E–F · 4701 Å² buried · 58 hydrogen bonds · protein-protein
Q–R · 4297 Å² buried · 50 hydrogen bonds · protein-protein

Compared structures

5GM2 · Crystal structure of methyltransferase TleD complexed with SAH and teleocidin A1 · the same entry in another collection · chain D against D, TM-score 1.00

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 A0A077K7L1
Elsewhere: RCSB PDB 5GM2 · PDBe 5GM2 · UniProt A0A077K7L1

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