Research workbench

Crystal structure of L-methionine-lyase from pseudomonas

Analyse Crystal structure of L-methionine-lyase from pseudomonas in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2O7C
Type: protein
Length: 1,592 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methionine gamma-lyase
EC: 4.4.1.11
UniProt: P13254
Ligands: SO4
Pockets: 9 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Methionine gamma-lyase (EC 4.4.1.11)	protein	398	42% helix, 17% strand	P13254

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D

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

Pockets

9 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	651	0.86	0.90	93	empty
2	487	0.75	0.83	38	SO4
3	577	0.74	0.81	54	SO4
4	519	0.73	0.81	41	SO4
5	584	0.72	0.79	49	SO4

Interfaces

6 interfaces between chains.

A–B · 2602 Å² buried · 44 hydrogen bonds · protein-protein
C–D · 2581 Å² buried · 46 hydrogen bonds · protein-protein
A–C · 1820 Å² buried · 21 hydrogen bonds · protein-protein
B–D · 1769 Å² buried · 28 hydrogen bonds · protein-protein
A–D · 744 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (cofactor).

Compared structures

2O7C · Crystal structure of L-methionine-lyase from Pseudomonas · the same entry in another collection · chain A against A, TM-score 1.00
P13254 · AlphaFold monomer V2.0 prediction for L-methionine gamma-lyase (P13254) · 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 P13254
Elsewhere: RCSB PDB 2O7C · PDBe 2O7C · UniProt P13254

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.