MolNFT v1 · #119334 · protein

Crystal structure of GP37(DIP) from bacteriophage phikz

5FT0: “Crystal structure of GP37(DIP) from bacteriophage phikz”. X-ray diffraction, 2 ligands (ARG, K), 9 pockets (best druggability 0.60). MolNFT v1 #119334 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5FT0
Type: protein
Length: 508 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GP37
UniProt: Q8SDC5
Ligands: ARG, K
Pockets: 9 · best druggability 0.60

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	GP37	protein	255	35% helix, 33% strand	Q8SDC5
B	GP37	protein	253	36% helix, 33% strand	Q8SDC5

Ligands and binding sites

ARG · Arginine · ligand · 2 copies · chains A, B
K · Potassium ion · metal · 2 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	202	0.60	0.81	26	empty
2	251	0.58	0.79	35	empty
3	111	0.55	0.84	24	empty
4	180	0.51	0.78	22	empty
5	174	0.46	0.75	22	empty

Interfaces

1 interface between chains.

A–B · 1214 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 modified (engineered).

Compared structures

5FT0 · Crystal structure of gp37(Dip) from bacteriophage phiKZ · the same entry in another collection · chain B against B, 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 Q8SDC5
Elsewhere: RCSB PDB 5FT0 · PDBe 5FT0 · UniProt Q8SDC5

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