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Convergent solutions to vhh domain stabilization from natural and in vitro evolution

Analyse Convergent solutions to vhh domain stabilization from natural and in vitro… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1SHM
Type: protein
Length: 466 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antibody rig
Pockets: 3 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 4% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Antibody rig	protein	118	5% helix, 53% strand	—
B	Antibody rig	protein	117	3% helix, 54% strand	—
D	Antibody rig	protein	113	5% helix, 54% strand	—

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	945	0.73	0.77	91	empty
2	68	0.53	0.86	18	empty
3	77	0.45	0.81	13	empty

Interfaces

4 interfaces between chains.

B–E · 536 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 485 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 424 Å² buried · 8 hydrogen bonds · protein-protein
D–E · 264 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

1SHM · Convergent solutions to VHH domain stabilization from natural and in vitro evolution · the same entry in another collection · chain D against D, 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 1SHM · PDBe 1SHM

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