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The crystal structure of the JACKDAW/IDD10 bound to the heterodimeric shr-scr complex

Analyse The crystal structure of the JACKDAW/IDD10 bound to the heterodimeric shr-scr… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5B3H
Type: protein
Length: 1,650 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein scarecrow; Protein short-root; Zinc finger protein jackdaw
UniProt: Q9M384, Q9SZF7, Q700D2
Ligands: ZN
Pockets: 19 · best druggability 0.84

Structure

x-ray diffraction · 6 distinct chains · 51% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein scarecrow	protein	368	53% helix, 16% strand	Q9M384
B	Protein short-root	protein	406	51% helix, 16% strand	Q9SZF7
D	Protein scarecrow	protein	368	52% helix, 16% strand	Q9M384
E	Protein short-root	protein	401	51% helix, 16% strand	Q9SZF7
C	Zinc finger protein jackdaw	protein	54	37% helix, 15% strand	Q700D2
F	Zinc finger protein jackdaw	protein	53	38% helix, 8% strand	Q700D2

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains C, F

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

Pockets

19 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	985	0.84	0.85	76	empty
2	1145	0.83	0.84	74	empty
3	257	0.82	0.94	37	empty
4	306	0.82	0.92	35	empty
5	760	0.80	0.83	88	empty

Interfaces

6 interfaces between chains.

D–E · 2013 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 1934 Å² buried · 20 hydrogen bonds · protein-protein
E–F · 963 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 963 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 579 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

5B3H · The crystal structure of the JACKDAW/IDD10 bound to the heterodimeric SHR-SCR complex · the same entry in another collection · chain F against F, TM-score 1.00
Q9SZF7 · AlphaFold monomer V2.0 prediction for protein short-root (Q9SZF7) · a predicted model of the same protein · chain B against A, TM-score 1.00
Q9M384 · AlphaFold monomer V2.0 prediction for protein scarecrow (Q9M384) · a predicted model of the same protein · chain A against A, TM-score 1.00
Q700D2 · AlphaFold monomer V2.0 prediction for zinc finger protein jackdaw (Q700D2) · a predicted model of the same protein · chain F against A, TM-score 0.55

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 Q9M384
Every structure of UniProt Q9SZF7
Every structure of UniProt Q700D2
Elsewhere: RCSB PDB 5B3H · PDBe 5B3H · UniProt Q9M384 · UniProt Q9SZF7 · UniProt Q700D2

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