Research workbench

Tail assembly of the phicrAss001 virion with C6 symmetry imposed

Analyse Tail assembly of the phicrAss001 virion with C6 symmetry imposed in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7QOL
Type: protein
Length: 6,371 residues
Chains: 30
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.33
Source: Bacteroides phage crAss001
Molecule: Portal protein gp20; Ring protein 1 gp43; Ring protein 2 gp40; Ring protein 3 gp35; Ring…
UniProt: A0A385DT68, A0A385DT91, A0A385DT87, A0A385DV73, A0A385DVC3, A0A385DTH1, A0A385DVM6, A0A385DVT1, A0A385DV85, A0A385DVD6
Ligands: MG
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · resolution 3.33 · 15 distinct chains · 29% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, O	Portal protein gp20	protein	657	53% helix, 15% strand	A0A385DT68
B, Q	Ring protein 1 gp43	protein	226	38% helix, 20% strand	A0A385DT91
C, S	Ring protein 2 gp40	protein	225	32% helix, 18% strand	A0A385DT87
D, T	Ring protein 3 gp35	protein	226	31% helix, 25% strand	A0A385DV73
E, F, U, V	Ring protein 4/5 gp34	protein	238	34% helix, 22% strand	A0A385DVC3
G	Tail hub protein A gp38	protein	177	32% helix, 23% strand	A0A385DTH1
H, Z	Tail hub protein A gp38	protein	188	29% helix, 26% strand	A0A385DTH1
I, a	Tail hub protein B gp39	protein	107	50% helix, 2% strand	A0A385DVM6
J, K, b, c	Tail fiber protein gp22	protein	19	74% helix, 0% strand	A0A385DVT1
L, d	Tail fiber protein gp22	protein	25	56% helix, 4% strand	A0A385DVT1
M, e	Cargo protein 1 gp45	protein	126	38% helix, 13% strand	A0A385DV85
N, f	Cargo protein 1 gp45	protein	32	53% helix, 0% strand	A0A385DV85
W	Tail hub protein A gp38	protein	174	34% helix, 23% strand	A0A385DTH1
P	Muzzle protein gp44	protein	1354	8% helix, 39% strand	A0A385DVD6
R	Muzzle bound helix	protein	14	50% helix, 0% strand	—

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, O

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	958	0.89	0.91	90	empty
2	884	0.87	0.89	83	empty
3	517	0.83	0.89	60	empty
4	839	0.82	0.85	75	empty
5	827	0.82	0.84	78	empty

Interfaces

88 interfaces between chains.

A–O · 6153 Å² buried · 77 hydrogen bonds · protein-protein
E–U · 2594 Å² buried · 32 hydrogen bonds · protein-protein
F–V · 2542 Å² buried · 29 hydrogen bonds · protein-protein
C–S · 2297 Å² buried · 26 hydrogen bonds · protein-protein
B–Q · 2209 Å² buried · 35 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 15 disulfide (disulfide).

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 A0A385DT68
Every structure of UniProt A0A385DT91
Every structure of UniProt A0A385DT87
Every structure of UniProt A0A385DV73
Every structure of UniProt A0A385DVC3
Every structure of UniProt A0A385DTH1
Every structure of UniProt A0A385DVM6
Every structure of UniProt A0A385DVT1
Every structure of UniProt A0A385DV85
Every structure of UniProt A0A385DVD6
Elsewhere: RCSB PDB 7QOL · PDBe 7QOL · UniProt A0A385DT68 · UniProt A0A385DT91 · UniProt A0A385DT87 · UniProt A0A385DV73 · UniProt A0A385DVC3 · UniProt A0A385DTH1 · UniProt A0A385DVM6 · UniProt A0A385DVT1 · UniProt A0A385DV85 · UniProt A0A385DVD6

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