MolNFT v1 · #73337 · protein

Crystal structure of a putative glycyl-glycine endopeptidase lytm (RUMGNA_02482) from ruminococcus gnavus atcc 29149 at 1.60 a resolution

3NYY: “Crystal structure of a putative glycyl-glycine endopeptidase lytm (RUMGNA_02482) from ruminococcus gnavus…”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.27). MolNFT v1 #73337 on GenesisL1: 3D structure, binding…

PDB: 3NYY
Type: protein
Length: 251 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative glycyl-glycine endopeptidase lytm
UniProt: A7B4J8
Ligands: SO4
Pockets: 2 · best druggability 0.27

Structure

x-ray diffraction · 1 distinct chain · 25% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative glycyl-glycine endopeptidase lytm	protein	251	25% helix, 24% strand	A7B4J8

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A
2PE · Nonaethylene glycol · additive · 3 copies · chains A

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	51	0.27	0.74	19	empty
2	57	0.26	0.73	19	empty

Modifications

Observed in the structure: 6 modified (engineered).

Compared structures

3NYY · Crystal structure of a putative glycyl-glycine endopeptidase lytM (RUMGNA_02482) from… · 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 A7B4J8
Elsewhere: RCSB PDB 3NYY · PDBe 3NYY · UniProt A7B4J8

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