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Crystal structure of the core FH2 domain of mouse MDIA1

Analyse Crystal structure of the core FH2 domain of mouse MDIA1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1V9D
Type: protein
Length: 1,207 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Diaphanous protein homolog 1
UniProt: O08808
Ligands: SO4
Pockets: 18 · best druggability 0.67

Structure

x-ray diffraction · 4 distinct chains · 72% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Diaphanous protein homolog 1	protein	308	74% helix, 1% strand	O08808
B	Diaphanous protein homolog 1	protein	321	70% helix, 1% strand	O08808
C	Diaphanous protein homolog 1	protein	278	71% helix, 0% strand	O08808
D	Diaphanous protein homolog 1	protein	300	71% helix, 0% strand	O08808

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains A, B, C

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

Pockets

18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	157	0.67	0.88	20	empty
2	141	0.66	0.87	18	empty
3	163	0.59	0.82	22	empty
4	148	0.59	0.83	24	empty
5	233	0.55	0.78	25	empty

Interfaces

4 interfaces between chains.

C–D · 1198 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1182 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 743 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 686 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

1V9D · Crystal structure of the core FH2 domain of mouse mDia1 · the same entry in another collection · chain D against D, TM-score 1.00
O08808 · AlphaFold monomer V2.0 prediction for protein diaphanous homolog 1 (O08808) · a predicted model of the same protein · chain C against A, TM-score 0.97

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 1V9D · PDBe 1V9D · UniProt O08808

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