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Human adenovirus type 21 knob in complex with domains SCR1 and SCR2 of CD46 (membrane cofactor protein, mcp)

Analyse Human adenovirus type 21 knob in complex with domains SCR1 and SCR2 of CD46… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3L89
Type: protein
Length: 3,715 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fiber protein; Membrane cofactor protein
UniProt: Q2KS96, P15529
Ligands: NAG
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 12 distinct chains · 5% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Fiber protein	protein	183	7% helix, 43% strand	Q2KS96
B	Fiber protein	protein	184	7% helix, 42% strand	Q2KS96
C	Fiber protein	protein	184	7% helix, 42% strand	Q2KS96
E	Fiber protein	protein	184	5% helix, 44% strand	Q2KS96
F, K	Fiber protein	protein	185	5% helix, 44% strand	Q2KS96
G	Fiber protein	protein	182	8% helix, 42% strand	Q2KS96
H	Fiber protein	protein	183	8% helix, 43% strand	Q2KS96
I, L	Fiber protein	protein	186	8% helix, 42% strand	Q2KS96
J	Fiber protein	protein	182	5% helix, 41% strand	Q2KS96
M, N, O, P, R, S, U, V, X	Membrane cofactor protein	protein	126	2% helix, 40% strand	P15529
Q, W	Membrane cofactor protein	protein	125	0% helix, 40% strand	P15529
T	Membrane cofactor protein	protein	124	0% helix, 35% strand	P15529

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains M, Q, N, P, S, V

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	351	0.84	0.93	41	empty
2	363	0.84	0.93	41	empty
3	361	0.83	0.92	44	empty
4	354	0.83	0.92	43	empty
5	1127	0.75	0.78	90	empty

Interfaces

45 interfaces between chains.

J–L · 1061 Å² buried · 9 hydrogen bonds · protein-protein
J–K · 1058 Å² buried · 9 hydrogen bonds · protein-protein
K–L · 1049 Å² buried · 9 hydrogen bonds · protein-protein
D–E · 1040 Å² buried · 10 hydrogen bonds · protein-protein
D–F · 1038 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 48 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

3L89 · Human Adenovirus type 21 knob in complex with domains SCR1 and SCR2 of CD46 (membrane… · the same entry in another collection · chain H against H, 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 Q2KS96
Every structure of UniProt P15529
Elsewhere: RCSB PDB 3L89 · PDBe 3L89 · UniProt Q2KS96 · UniProt P15529

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