Research workbench

Adenovirus 3 head domain mutant V239D

Analyse Adenovirus 3 head domain mutant V239D in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4WYJ
Type: protein
Length: 566 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fiber protein
UniProt: P04501
Ligands: SO4
Pockets: 5 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Fiber protein	protein	189	6% helix, 39% strand	P04501
C	Fiber protein	protein	188	6% helix, 41% strand	P04501

Ligands and binding sites

SO4 · Sulfate ion · ion · 10 copies · chains A, B, C

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	460	0.83	0.91	42	empty
2	55	0.62	0.93	15	empty
3	57	0.60	0.91	17	empty
4	252	0.49	0.74	32	empty
5	64	0.33	0.76	19	empty

Interfaces

3 interfaces between chains.

B–C · 978 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 970 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 937 Å² buried · 4 hydrogen bonds · protein-protein

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 P04501
Elsewhere: RCSB PDB 4WYJ · PDBe 4WYJ · UniProt P04501

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