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Engineered digoxigenin binder DIG10.3

Analyse Engineered digoxigenin binder DIG10.3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4J9A
Type: protein
Length: 1,052 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Engineered digoxigenin binder protein DIG10.3
UniProt: Q9HYR3
Ligands: DOG
Pockets: 11 · best druggability 0.86

Structure

x-ray diffraction · 8 distinct chains · 28% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Engineered digoxigenin binder protein DIG10.3	protein	122	25% helix, 43% strand	Q9HYR3
B	Engineered digoxigenin binder protein DIG10.3	protein	121	26% helix, 45% strand	Q9HYR3
D	Engineered digoxigenin binder protein DIG10.3	protein	124	26% helix, 43% strand	Q9HYR3
E	Engineered digoxigenin binder protein DIG10.3	protein	111	29% helix, 41% strand	Q9HYR3
F	Engineered digoxigenin binder protein DIG10.3	protein	123	29% helix, 42% strand	Q9HYR3
G	Engineered digoxigenin binder protein DIG10.3	protein	105	30% helix, 32% strand	Q9HYR3
H	Engineered digoxigenin binder protein DIG10.3	protein	113	28% helix, 36% strand	Q9HYR3
I	Engineered digoxigenin binder protein DIG10.3	protein	111	29% helix, 34% strand	Q9HYR3

Ligands and binding sites

DOG · Digoxigenin · ligand · 9 copies · chains A, B, C, D, E, F, G, H, I

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

Pockets

11 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1086	0.86	0.87	116	DOG
2	723	0.82	0.85	53	DOG
3	581	0.77	0.83	48	DOG
4	747	0.77	0.81	75	DOG
5	417	0.76	0.85	47	DOG

Interfaces

8 interfaces between chains.

C–F · 674 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 634 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 573 Å² buried · 2 hydrogen bonds · protein-protein
E–F · 459 Å² buried · 0 hydrogen bonds · protein-protein
C–D · 424 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4J9A · Engineered Digoxigenin binder DIG10.3 · the same entry in another collection · chain I against I, TM-score 1.00
Q9HYR3 · AlphaFold monomer V2.0 prediction for uncharacterized PHZA/B-like protein PA3332 (Q9HYR3) · a predicted model of the same protein · chain I against A, TM-score 0.96

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 Q9HYR3
Elsewhere: RCSB PDB 4J9A · PDBe 4J9A · UniProt Q9HYR3

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