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Structure-function analysis of receptor binding in adeno-associated virus serotype 6 (aav-6)

Analyse Structure-function analysis of receptor binding in adeno-associated virus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3SHM
Type: protein
Length: 10,320 residues
Chains: 20
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Capsid protein VP1
UniProt: O56137
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T	Capsid protein VP1	protein	516	5% helix, 32% strand	O56137

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	427	0.79	0.88	36	empty
2	416	0.79	0.88	35	empty
3	444	0.79	0.87	34	empty
4	446	0.79	0.87	35	empty
5	417	0.79	0.88	35	empty

Interfaces

45 interfaces between chains.

F–P · 5211 Å² buried · 88 hydrogen bonds · protein-protein
K–R · 5203 Å² buried · 86 hydrogen bonds · protein-protein
N–Q · 5202 Å² buried · 87 hydrogen bonds · protein-protein
F–I · 5201 Å² buried · 87 hydrogen bonds · protein-protein
H–N · 5199 Å² buried · 86 hydrogen bonds · protein-protein

Compared structures

3SHM · Structure-function Analysis of Receptor Binding in Adeno-Associated Virus Serotype 6… · the same entry in another collection · chain A against A, TM-score 1.00

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Every structure of UniProt O56137
Elsewhere: RCSB PDB 3SHM · PDBe 3SHM · UniProt O56137

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