MolNFT v1 · #18166 · protein

Crystal structure of L-methionine alpha-, gamma-lyase

1PG8 · Methionine gamma-lyase: “Crystal structure of L-methionine alpha-, gamma-lyase”. X-ray diffraction, 2 ligands (PLP, SO4), 14 pockets (best druggability 0.84). MolNFT v1 #18166 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 1PG8
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: PLP, SO4
Pockets: 14 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Methionine gamma-lyase (EC 4.4.1.11)	protein	398	43% helix, 16% strand	P13254

Ligands and binding sites

PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, C, B, D
SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
PEG · Di(hydroxyethyl)ether · additive · 11 copies · chains A, D, B, C

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

Pockets

14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	717	0.84	0.88	105	PEG
2	595	0.76	0.82	77	SO4, PLP
3	576	0.75	0.82	73	SO4, PLP
4	61	0.72	0.98	25	PLP
5	449	0.71	0.82	49	SO4

Interfaces

6 interfaces between chains.

A–C · 2681 Å² buried · 39 hydrogen bonds · protein-protein
B–D · 2650 Å² buried · 42 hydrogen bonds · protein-protein
A–D · 1637 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 1618 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 764 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).

Compared structures

1PG8 · Crystal Structure of L-methionine alpha-, gamma-lyase · 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 1PG8 · PDBe 1PG8 · UniProt P13254

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