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P4 protein from bacteriophage PHI12 R279A mutant in complex with ATP

Analyse P4 protein from bacteriophage PHI12 R279A mutant in complex with ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2VHT
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: ATP
Pockets: 11 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 29% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	NTPase P4	protein	304	29% helix, 30% strand	Q94M05

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, B, C

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

Pockets

11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	472	0.82	0.89	51	ATP
2	479	0.81	0.88	52	ATP
3	662	0.78	0.84	70	empty
4	744	0.78	0.82	68	empty
5	361	0.71	0.83	44	empty

Interfaces

2 interfaces between chains.

A–B · 2038 Å² buried · 29 hydrogen bonds · protein-protein
B–C · 2036 Å² buried · 27 hydrogen bonds · protein-protein

Compared structures

2VHT · P4 PROTEIN FROM BACTERIOPHAGE PHI12 R279A mutant in complex with ATP · 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 2VHT · PDBe 2VHT · UniProt Q94M05

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