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The conformations and interactions of the four-layer aggregate revealed by X-ray crystallography diffraction implied the importance of peptides at opposite ends in their assemblies

Analyse The conformations and interactions of the four-layer aggregate revealed by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4GQH
Type: protein
Length: 4,690 residues
Chains: 34
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Capsid protein
UniProt: P69687
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 20 distinct chains · 50% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Capsid protein	protein	142	51% helix, 11% strand	P69687
B	Capsid protein	protein	139	53% helix, 10% strand	P69687
C	Capsid protein	protein	144	50% helix, 8% strand	P69687
D	Capsid protein	protein	143	50% helix, 10% strand	P69687
E, O	Capsid protein	protein	140	49% helix, 11% strand	P69687
F, K	Capsid protein	protein	143	46% helix, 13% strand	P69687
G	Capsid protein	protein	143	48% helix, 11% strand	P69687
H	Capsid protein	protein	144	50% helix, 11% strand	P69687
I, L	Capsid protein	protein	141	50% helix, 10% strand	P69687
J	Capsid protein	protein	145	52% helix, 11% strand	P69687
M, N	Capsid protein	protein	142	51% helix, 10% strand	P69687
P	Capsid protein	protein	147	50% helix, 11% strand	P69687
Q	Capsid protein	protein	146	51% helix, 12% strand	P69687
R, S, U	Capsid protein	protein	133	50% helix, 12% strand	P69687
T	Capsid protein	protein	132	49% helix, 12% strand	P69687
V, W, Z, d, e, f, h, i	Capsid protein	protein	134	51% helix, 12% strand	P69687
X	Capsid protein	protein	131	52% helix, 14% strand	P69687
Y, b	Capsid protein	protein	132	50% helix, 11% strand	P69687
a	Capsid protein	protein	131	52% helix, 14% strand	P69687
c	Capsid protein	protein	136	47% helix, 13% strand	P69687

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	1012	0.82	0.83	86	empty
2	866	0.82	0.84	91	empty
3	768	0.80	0.83	81	empty
4	806	0.80	0.83	80	empty
5	1177	0.80	0.81	94	empty

Interfaces

66 interfaces between chains.

F–G · 1286 Å² buried · 15 hydrogen bonds · protein-protein
P–Q · 1228 Å² buried · 19 hydrogen bonds · protein-protein
J–L · 1184 Å² buried · 17 hydrogen bonds · protein-protein
I–Q · 1180 Å² buried · 18 hydrogen bonds · protein-protein
K–M · 1178 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

4GQH · The Conformations and Interactions of the Four-Layer Aggregate Revealed by X-ray… · the same entry in another collection · chain B against B, 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 P69687
Elsewhere: RCSB PDB 4GQH · PDBe 4GQH · UniProt P69687

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