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Structure of cabbcii-10 nanobody

Analyse Structure of cabbcii-10 nanobody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3DWT
Type: protein
Length: 1,000 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cabbcii-10
Pockets: 4 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 10% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Cabbcii-10	protein	125	10% helix, 49% strand	—

Ligands and binding sites

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	203	0.63	0.83	34	empty
2	100	0.43	0.78	34	empty
3	58	0.39	0.80	16	empty
4	83	0.31	0.73	27	empty

Interfaces

12 interfaces between chains.

B–C · 613 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 606 Å² buried · 9 hydrogen bonds · protein-protein
D–E · 328 Å² buried · 9 hydrogen bonds · protein-protein
B–F · 326 Å² buried · 11 hydrogen bonds · protein-protein
C–G · 320 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

3DWT · Structure of CabBCII-10 nanobody · 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 3DWT · PDBe 3DWT

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