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P4 protein from PHI12 in complex with ampcpp and mn

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

PDB: 1W4A
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, MN
Pockets: 7 · best druggability 0.85

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	NTPase P4	protein	304	32% helix, 30% strand	Q94M05

Ligands and binding sites

APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 3 copies · chains A, B, C
MN · Manganese (II) ion · metal · 3 copies · chains A, B, C

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

Pockets

7 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	1155	0.85	0.86	134	APC, MN
2	724	0.78	0.82	65	empty
3	746	0.77	0.81	65	empty
4	356	0.55	0.75	47	empty
5	81	0.33	0.74	18	empty

Interfaces

2 interfaces between chains.

B–C · 1955 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 1945 Å² buried · 27 hydrogen bonds · protein-protein

Compared structures

1W4A · P4 protein from PHI12 in complex with AMPcPP and Mn · 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 1W4A · PDBe 1W4A · UniProt Q94M05

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