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P4 protein from bacteriophage PHI12 S252A mutant in complex with ADP

Analyse P4 protein from bacteriophage PHI12 S252A mutant in complex with ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2VHJ
Type: protein
Length: 864 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NTPase P4
UniProt: Q94M05
Ligands: ADP
Pockets: 11 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	NTPase P4	protein	288	30% helix, 32% strand	Q94M05

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · 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, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1048	0.81	0.82	128	empty
2	593	0.77	0.83	62	empty
3	224	0.67	0.85	45	ADP
4	220	0.67	0.85	45	ADP
5	376	0.57	0.75	50	empty

Interfaces

2 interfaces between chains.

B–C · 1858 Å² buried · 28 hydrogen bonds · protein-protein
A–B · 1832 Å² buried · 27 hydrogen bonds · protein-protein

Compared structures

2VHJ · P4 PROTEIN FROM BACTERIOPHAGE PHI12 S252A mutant in complex with ADP · 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 2VHJ · PDBe 2VHJ · UniProt Q94M05

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