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Crystal structure of the designed antibody desab-anti-hsa-P1

Analyse Crystal structure of the designed antibody desab-anti-hsa-P1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6Z3X
Type: protein
Length: 240 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Desab-anti-hsa-P1
Ligands: NA
Pockets: 3 · best druggability 0.50

Structure

x-ray diffraction · 2 distinct chains · 10% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Desab-anti-hsa-P1	protein	119	13% helix, 55% strand	—
B	Desab-anti-hsa-P1	protein	121	7% helix, 51% strand	—

Ligands and binding sites

NA · Sodium ion · metal · chains B
CAC · Cacodylate ion · additive · 6 copies · chains A, B
IMD · Imidazole · additive · chains B

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	224	0.50	0.75	24	CAC
2	80	0.35	0.76	20	empty
3	59	0.27	0.73	16	IMD

Interfaces

1 interface between chains.

A–B · 624 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

6Z3X · Crystal structure of the designed antibody DesAb-anti-HSA-P1 · 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 6Z3X · PDBe 6Z3X

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