Research workbench

Adenovirus species D serotype 49 fiber-knob KO1 mutant

Analyse Adenovirus species D serotype 49 fiber-knob KO1 mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6QPO
Type: protein
Length: 1,200 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fiber
UniProt: Q09TX9
Ligands: SO4
Pockets: 9 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 9% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Fiber	protein	200	9% helix, 40% strand	Q09TX9

Ligands and binding sites

SO4 · Sulfate ion · ion · chains A, C

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

Pockets

9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	973	0.80	0.82	97	empty
2	337	0.78	0.88	35	empty
3	319	0.77	0.88	36	empty
4	242	0.53	0.77	35	empty
5	55	0.51	0.87	18	empty

Interfaces

10 interfaces between chains.

D–E · 1356 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1281 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 1277 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 1269 Å² buried · 19 hydrogen bonds · protein-protein
D–F · 1224 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

6QPO · Adenovirus species D serotype 49 Fiber-Knob KO1 mutant · 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 Q09TX9
Elsewhere: RCSB PDB 6QPO · PDBe 6QPO · UniProt Q09TX9

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