Research workbench

X-ray structure of the entire lipid-containing bacteriophage PM2

Analyse X-ray structure of the entire lipid-containing bacteriophage PM2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2W0C
Type: protein
Length: 3,424 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Major capsid protein P2; Protein 2; Protein P3; Protein P6
UniProt: P15794, Q9XJR3, Q9XJR6, Q9XJR1
Ligands: CA
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 7 distinct chains · 28% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J	Major capsid protein P2	protein	269	12% helix, 47% strand	P15794
L	Protein 2	protein	335	9% helix, 43% strand	Q9XJR3
P	Protein P3	protein	65	42% helix, 2% strand	Q9XJR6
Q	Protein P3	protein	60	47% helix, 3% strand	Q9XJR6
R	Protein P3	protein	63	44% helix, 6% strand	Q9XJR6
S	Protein P3	protein	84	70% helix, 5% strand	Q9XJR6
T	Protein P6	protein	127	63% helix, 0% strand	Q9XJR1

Ligands and binding sites

CA · Calcium ion · metal · 11 copies · chains A, B, C, Q, D, E, R, F, G, P, H, I, S, J, L

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	615	0.85	0.90	96	empty
2	990	0.85	0.86	93	empty
3	757	0.78	0.82	54	empty
4	194	0.74	0.91	28	empty
5	213	0.74	0.90	30	empty

Interfaces

41 interfaces between chains.

E–R · 1449 Å² buried · 21 hydrogen bonds · protein-protein
C–Q · 1286 Å² buried · 12 hydrogen bonds · protein-protein
D–E · 1223 Å² buried · 20 hydrogen bonds · protein-protein
I–J · 1220 Å² buried · 20 hydrogen bonds · protein-protein
D–F · 1218 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

2W0C · X-ray structure of the entire lipid-containing bacteriophage PM2 · 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 P15794
Every structure of UniProt Q9XJR3
Every structure of UniProt Q9XJR6
Every structure of UniProt Q9XJR1
Elsewhere: RCSB PDB 2W0C · PDBe 2W0C · UniProt P15794 · UniProt Q9XJR3 · UniProt Q9XJR6 · UniProt Q9XJR1

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