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Autoinhibited formin MDIA1 structure

Analyse Autoinhibited formin MDIA1 structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3OBV
Type: protein
Length: 2,967 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein diaphanous homolog 1
UniProt: O08808
Ligands: GLC, FRU
Pockets: 20 · best druggability 0.72

Structure

x-ray diffraction · 7 distinct chains · 68% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Protein diaphanous homolog 1	protein	322	72% helix, 2% strand	O08808
E	Protein diaphanous homolog 1	protein	419	65% helix, 2% strand	O08808
B	Protein diaphanous homolog 1	protein	319	72% helix, 2% strand	O08808
F	Protein diaphanous homolog 1	protein	419	67% helix, 2% strand	O08808
G	Protein diaphanous homolog 1	protein	420	66% helix, 2% strand	O08808
D	Protein diaphanous homolog 1	protein	327	72% helix, 2% strand	O08808
H	Protein diaphanous homolog 1	protein	419	66% helix, 2% strand	O08808

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
FRU · beta-D-fructofuranose · sugar · 8 copies · chains A, B, C, D

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

Pockets

20 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	976	0.72	0.76	116	empty
2	675	0.69	0.77	57	GLC, FRU
3	514	0.67	0.78	45	empty
4	61	0.57	0.89	20	empty
5	285	0.55	0.76	28	empty

Interfaces

11 interfaces between chains.

G–H · 3969 Å² buried · 24 hydrogen bonds · protein-protein
E–F · 3932 Å² buried · 26 hydrogen bonds · protein-protein
C–D · 3614 Å² buried · 32 hydrogen bonds · protein-protein
A–B · 3596 Å² buried · 31 hydrogen bonds · protein-protein
A–F · 1609 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

3OBV · Autoinhibited Formin mDia1 Structure · the same entry in another collection · chain H against H, TM-score 1.00
O08808 · AlphaFold monomer V2.0 prediction for protein diaphanous homolog 1 (O08808) · a predicted model of the same protein · chain G against A, TM-score 0.85

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 O08808
Elsewhere: RCSB PDB 3OBV · PDBe 3OBV · UniProt O08808

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