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Darpin-based crystallization chaperones exploit molecular geometry as a screening dimension in protein crystallography

Analyse Darpin-based crystallization chaperones exploit molecular geometry as a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5AQA
Type: protein
Length: 819 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: OFF7_DB04V3
Ligands: SCN
Pockets: 6 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	OFF7_DB04V3	protein	412	46% helix, 12% strand	—
B	OFF7_DB04V3	protein	407	44% helix, 12% strand	—

Ligands and binding sites

SCN · Thiocyanate ion · ion · 4 copies · chains A, B

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

Pockets

6 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	1098	0.82	0.83	94	SCN
2	56	0.51	0.87	16	empty
3	66	0.46	0.83	14	SCN
4	120	0.41	0.76	22	empty
5	79	0.33	0.74	19	empty

Interfaces

1 interface between chains.

A–B · 727 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5AQA · DARPin-based Crystallization Chaperones exploit Molecular Geometry as a Screening… · 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 5AQA · PDBe 5AQA

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