MolNFT v1 · #25738 · protein

P4 protein from bacteriophage PHI12 in complex with ampcpp

1W48 · NTPase P4: “P4 protein from bacteriophage PHI12 in complex with ampcpp”. X-ray diffraction, 1 ligand (APC), 9 pockets (best druggability 0.78). MolNFT v1 #25738 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1W48
Type: protein
Length: 912 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NTPase P4
UniProt: Q94M05
Ligands: APC
Pockets: 9 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	NTPase P4	protein	304	33% helix, 32% strand	Q94M05

Ligands and binding sites

APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 3 copies · chains A, B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	752	0.78	0.82	69	empty
2	680	0.78	0.83	63	empty
3	683	0.76	0.82	70	empty
4	382	0.75	0.86	51	APC
5	330	0.74	0.86	43	APC

Interfaces

2 interfaces between chains.

A–B · 1927 Å² buried · 26 hydrogen bonds · protein-protein
B–C · 1909 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

1W48 · P4 protein from Bacteriophage PHI12 in complex with AMPcPP · 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 Q94M05
Elsewhere: RCSB PDB 1W48 · PDBe 1W48 · UniProt Q94M05

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