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Structure of a zn-bound camelid single domain antibody

Analyse Structure of a zn-bound camelid single domain antibody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6KSN
Type: protein
Length: 266 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ICAB3
Ligands: ZN, NA
Pockets: 2 · best druggability 0.56

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ICAB3	protein	134	7% helix, 48% strand	—
B	ICAB3	protein	132	7% helix, 51% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B
NA · Sodium ion · metal · chains B
EDO · 1,2-ethanediol · additive · 18 copies · chains A, B

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

Pockets

2 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	62	0.56	0.88	16	EDO
2	113	0.39	0.75	20	empty

Interfaces

1 interface between chains.

A–B · 689 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

6KSN · Structure of a Zn-bound camelid single domain antibody · 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 6KSN · PDBe 6KSN

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