MolNFT v1 · #18137 · protein

Crystal structure of homocysteine alpha-, gamma-lyase at 1.8 ångströms

1PFF · Methionine gamma-lyase: “Crystal structure of homocysteine alpha-, gamma-lyase at 1.8 ångströms”. X-ray diffraction, 3 pockets (best druggability 0.71). MolNFT v1 #18137 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1PFF
Type: protein
Length: 662 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methionine gamma-lyase
EC: 4.4.1.11
UniProt: O15565
Pockets: 3 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Methionine gamma-lyase (EC 4.4.1.11)	protein	331	44% helix, 16% strand	O15565

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 21 copies · chains A, B
PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B

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

Pockets

3 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	486	0.71	0.81	55	EDO
2	521	0.70	0.80	61	EDO
3	78	0.31	0.73	14	empty

Interfaces

1 interface between chains.

A–B · 1291 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

1PFF · Crystal Structure of Homocysteine alpha-, gamma-lyase at 1.8 Angstroms · the same entry in another collection · chain A against A, 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 O15565
Elsewhere: RCSB PDB 1PFF · PDBe 1PFF · UniProt O15565

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