MolNFT v1 · #105817 · protein

Structure of the lactococcal phage 1358 receptor binding protein in complex with glcnac-1P

4RGG · Putative phage structural protein: “Structure of the lactococcal phage 1358 receptor binding protein in complex with glcnac-1P”. X-ray diffraction, 1 ligand (GN1), 6 pockets (best druggability 0.59). MolNFT v1 #105817 on GenesisL1…

PDB: 4RGG
Type: protein
Length: 780 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative phage structural protein
UniProt: D3W0F1
Ligands: GN1
Pockets: 6 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain · 9% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Putative phage structural protein	protein	390	9% helix, 42% strand	D3W0F1

Ligands and binding sites

GN1 · 2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucopyranose · ligand · 2 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	531	0.59	0.73	51	GN1
2	266	0.56	0.77	33	empty
3	250	0.52	0.76	25	empty
4	154	0.38	0.72	22	empty
5	54	0.31	0.75	14	empty

Interfaces

1 interface between chains.

A–B · 227 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

4RGG · Structure of the lactococcal phage 1358 receptor binding protein in complex with GlcNAc-1P · 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 D3W0F1
Elsewhere: RCSB PDB 4RGG · PDBe 4RGG · UniProt D3W0F1

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