MolNFT v1 · #12144 · protein

E. COLI meth C-terminal fragment (649-1227)

1K7Y · Methionine synthase: “E. COLI meth C-terminal fragment (649-1227)”. X-ray diffraction, 2 ligands (B12, SO4), 6 pockets (best druggability 0.72). MolNFT v1 #12144 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1K7Y
Type: protein
Length: 577 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methionine synthase
EC: 2.1.1.13
UniProt: P13009
Ligands: B12, SO4
Pockets: 6 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 48% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Methionine synthase (EC 2.1.1.13)	protein	577	48% helix, 13% strand	P13009

Ligands and binding sites

B12 · Cobalamin · ligand · chains A
SO4 · Sulfate ion · ion · 10 copies · chains A

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

Pockets

6 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	574	0.72	0.80	68	B12
2	217	0.63	0.82	40	empty
3	223	0.59	0.80	26	empty
4	61	0.33	0.77	14	empty
5	86	0.32	0.73	17	empty

Compared structures

1K7Y · E. coli MetH C-terminal fragment (649-1227) · the same entry in another collection · chain A against A, TM-score 1.00
P13009 · AlphaFold monomer V2.0 prediction for methionine synthase (P13009) · 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 P13009
Elsewhere: RCSB PDB 1K7Y · PDBe 1K7Y · UniProt P13009

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