Research workbench

Structure of native catalytic antibody HA5-19A4

Analyse Structure of native catalytic antibody HA5-19A4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1HQ4
Type: protein
Length: 862 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antibody HA5-19A4 Fab light chain; Antibody HA5-19A4 Fab heavy chain
UniProt: Q91W12, P01867
Ligands: CD
Pockets: 13 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 5% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Antibody HA5-19A4 Fab light chain	protein	215	7% helix, 50% strand	Q91W12
B, D	Antibody HA5-19A4 Fab heavy chain	protein	216	3% helix, 50% strand	P01867

Ligands and binding sites

CD · Cadmium ion · metal · 2 copies · chains A, C

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

Pockets

13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	900	0.74	0.78	102	empty
2	149	0.69	0.88	21	empty
3	146	0.68	0.88	19	empty
4	318	0.55	0.75	49	empty
5	282	0.52	0.75	35	empty

Interfaces

4 interfaces between chains.

C–D · 1851 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1839 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 579 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 63 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

1HQ4 · Structure of native catalytic antibody HA5-19A4 · the same entry in another collection · chain A against A, TM-score 1.00
P01867 · AlphaFold monomer V2.0 prediction for ig gamma-2B chain C region (P01867) · a predicted model of the same protein · chain B against A, TM-score 0.50

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q91W12
Every structure of UniProt P01867
Elsewhere: RCSB PDB 1HQ4 · PDBe 1HQ4 · UniProt Q91W12 · UniProt P01867

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