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Crystal structure of anti-influenza single-domain llama antibody SD38

Analyse Crystal structure of anti-influenza single-domain llama antibody SD38 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6CK8
Type: protein
Length: 372 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Llama antibody SD38
Ligands: SO4
Pockets: 4 · best druggability 0.57

Structure

x-ray diffraction · 1 distinct chain · 6% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Llama antibody SD38	protein	124	6% helix, 48% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 14 copies · chains A, B, C
1PE · Pentaethylene glycol · additive · 7 copies · chains A, B, C
GOL · Glycerol · additive · 2 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	171	0.57	0.81	32	1PE
2	165	0.47	0.76	24	1PE
3	124	0.40	0.75	22	SO4
4	53	0.33	0.78	17	SO4

Interfaces

2 interfaces between chains.

A–B · 592 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 581 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

6CK8 · Crystal structure of anti-influenza single-domain llama antibody SD38 · 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
Elsewhere: RCSB PDB 6CK8 · PDBe 6CK8

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