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Adomet complex of meth C-terminal fragment

Analyse Adomet complex of meth C-terminal fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1K98
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: 5 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Methionine synthase (EC 2.1.1.13)	protein	577	46% helix, 14% strand	P13009

Ligands and binding sites

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

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	818	0.76	0.80	82	B12
2	319	0.58	0.77	37	empty
3	203	0.46	0.74	31	empty
4	82	0.35	0.76	17	empty
5	71	0.33	0.76	15	empty

Compared structures

1K98 · AdoMet complex of MetH C-terminal fragment · 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 1K98 · PDBe 1K98 · UniProt P13009

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