Research workbench

SH3-II of drosophila rim-binding protein with APLIP1 peptide

Analyse SH3-II of drosophila rim-binding protein with APLIP1 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4Z88
Type: protein
Length: 911 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rim-binding protein, isoform F; Jnk-interacting protein 1
UniProt: A0A0B4JDC9, Q9W0K0
Ligands: PO4, NH2
Pockets: 12 · best druggability 0.71

Structure

x-ray diffraction · 18 distinct chains · 16% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Rim-binding protein, isoform F	protein	65	17% helix, 42% strand	A0A0B4JDC9
B, I	Rim-binding protein, isoform F	protein	66	17% helix, 41% strand	A0A0B4JDC9
C	Rim-binding protein, isoform F	protein	65	17% helix, 43% strand	A0A0B4JDC9
D, H	Rim-binding protein, isoform F	protein	70	16% helix, 40% strand	A0A0B4JDC9
E	Rim-binding protein, isoform F	protein	63	17% helix, 41% strand	A0A0B4JDC9
F	Rim-binding protein, isoform F	protein	67	16% helix, 40% strand	A0A0B4JDC9
G	Rim-binding protein, isoform F	protein	67	16% helix, 42% strand	A0A0B4JDC9
J, L	Rim-binding protein, isoform F	protein	68	16% helix, 41% strand	A0A0B4JDC9
K	Rim-binding protein, isoform F	protein	66	17% helix, 42% strand	A0A0B4JDC9
M	Jnk-interacting protein 1	protein	11	0% helix, 0% strand	Q9W0K0
N	Jnk-interacting protein 1	protein	5	0% helix, 0% strand	Q9W0K0
O	Jnk-interacting protein 1	protein	10	30% helix, 0% strand	Q9W0K0
P	Jnk-interacting protein 1	protein	8	0% helix, 0% strand	Q9W0K0
Q, S	Jnk-interacting protein 1	protein	13	23% helix, 0% strand	Q9W0K0
R	Jnk-interacting protein 1	protein	7	0% helix, 0% strand	Q9W0K0
T	Jnk-interacting protein 1	protein	5	0% helix, 0% strand	Q9W0K0
U, W	Jnk-interacting protein 1	protein	12	0% helix, 0% strand	Q9W0K0
V, X	Jnk-interacting protein 1	protein	7	0% helix, 0% strand	Q9W0K0

Ligands and binding sites

PO4 · Phosphate ion · ion · 11 copies · chains A, B, C, E, F, G, H, I, J, K, L
NH2 · Amino group · ion · 6 copies · chains F, M, O, Q, L, S, U, H, W

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

Pockets

12 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	243	0.71	0.87	37	empty
2	183	0.68	0.87	29	empty
3	212	0.68	0.85	28	empty
4	243	0.66	0.83	42	empty
5	199	0.65	0.85	33	empty

Interfaces

43 interfaces between chains.

G–S · 670 Å² buried · 8 hydrogen bonds · protein-protein
E–Q · 647 Å² buried · 6 hydrogen bonds · protein-protein
K–W · 617 Å² buried · 4 hydrogen bonds · protein-protein
I–U · 617 Å² buried · 9 hydrogen bonds · protein-protein
A–M · 594 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

4Z88 · SH3-II of Drosophila Rim-binding protein with Aplip1 peptide · 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
Every structure of UniProt A0A0B4JDC9
Every structure of UniProt Q9W0K0
Elsewhere: RCSB PDB 4Z88 · PDBe 4Z88 · UniProt A0A0B4JDC9 · UniProt Q9W0K0

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.