MolNFT v1 · #116223 · protein

The crystal structure of LY7917

5D74 · Putative phage lysin: “The crystal structure of LY7917”. X-ray diffraction, 2 ligands (NA, CL), 6 pockets (best druggability 0.51). MolNFT v1 #116223 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5D74
Type: protein
Length: 466 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative phage lysin
UniProt: M1PKZ3
Ligands: NA, CL
Pockets: 6 · best druggability 0.51

Structure

x-ray diffraction · 2 distinct chains · 16% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative phage lysin	protein	232	17% helix, 41% strand	M1PKZ3
B	Putative phage lysin	protein	234	15% helix, 41% strand	M1PKZ3

Ligands and binding sites

NA · Sodium ion · metal · 7 copies · chains A, B
CL · Chloride ion · ion · 6 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	228	0.51	0.76	29	NA
2	54	0.40	0.81	16	NA
3	123	0.39	0.74	27	NA
4	86	0.35	0.75	20	empty
5	69	0.32	0.75	18	empty

Interfaces

1 interface between chains.

A–B · 582 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5D74 · The crystal structure of Ly7917 · 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 M1PKZ3
Elsewhere: RCSB PDB 5D74 · PDBe 5D74 · UniProt M1PKZ3

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