MolNFT v1 · #92543 · protein

Crystal structure of the C-terminal domain of GP131 from bacteriophage phikz

4GBF · PHIKZ131: “Crystal structure of the C-terminal domain of GP131 from bacteriophage phikz”. X-ray diffraction, 2 ligands (MG, CL), 9 pockets (best druggability 0.79). MolNFT v1 #92543 on GenesisL1: 3D structure, binding sites and…

PDB: 4GBF
Type: protein
Length: 739 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: PHIKZ131
UniProt: Q8SD31
Ligands: MG, CL
Pockets: 9 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 15% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	PHIKZ131	protein	369	14% helix, 43% strand	Q8SD31
B	PHIKZ131	protein	370	16% helix, 42% strand	Q8SD31

Ligands and binding sites

MG · Magnesium ion · metal · 5 copies · chains A, B
CL · Chloride ion · ion · 4 copies · chains A, B

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

Pockets

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	460	0.79	0.87	58	MG
2	559	0.78	0.85	53	empty
3	276	0.65	0.81	38	empty
4	245	0.61	0.81	34	empty
5	130	0.50	0.79	19	empty

Interfaces

1 interface between chains.

A–B · 693 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

4GBF · Crystal structure of the C-terminal domain of gp131 from bacteriophage phiKZ · 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 Q8SD31
Elsewhere: RCSB PDB 4GBF · PDBe 4GBF · UniProt Q8SD31

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