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A viral CAPSID:ANTIBODY complex

Analyse A viral CAPSID:ANTIBODY complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5LDN
Type: protein
Length: 1,358 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hexon PROTEIN,HEXON capsid; Antibody
UniProt: P04133
Pockets: 16 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 11% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hexon PROTEIN,HEXON capsid	protein	927	16% helix, 28% strand	P04133
L	Antibody	protein	213	1% helix, 38% strand	—
H	Antibody	protein	218	3% helix, 42% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	100	0.76	0.97	26	empty
2	603	0.73	0.80	50	empty
3	525	0.70	0.80	78	empty
4	443	0.64	0.77	35	empty
5	344	0.63	0.79	35	empty

Interfaces

3 interfaces between chains.

L–H · 1781 Å² buried · 11 hydrogen bonds · protein-protein
A–H · 385 Å² buried · 4 hydrogen bonds · protein-protein
A–L · 45 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5LDN · A viral capsid:antibody complex · 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 P04133
Elsewhere: RCSB PDB 5LDN · PDBe 5LDN · UniProt P04133

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