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Crystal structure of complex between amino and carboxy terminal fragments of MDIA1
Analyse Crystal structure of complex between amino and carboxy terminal fragments of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3O4X
- Type
- protein
- Length
- 2,997 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein diaphanous homolog 1
- UniProt
- O08808
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 69% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein diaphanous homolog 1 | protein | 317 | 70% helix, 1% strand | O08808 |
| B | Protein diaphanous homolog 1 | protein | 318 | 69% helix, 1% strand | O08808 |
| C | Protein diaphanous homolog 1 | protein | 311 | 72% helix, 1% strand | O08808 |
| D | Protein diaphanous homolog 1 | protein | 319 | 71% helix, 1% strand | O08808 |
| E, H, G, F | Protein diaphanous homolog 1 | protein | 433 | 64% helix, 2% strand | O08808 |
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1096 | 0.75 | 0.78 | 107 | empty |
| 2 | 922 | 0.74 | 0.77 | 76 | empty |
| 3 | 858 | 0.72 | 0.77 | 65 | empty |
| 4 | 478 | 0.68 | 0.79 | 36 | empty |
| 5 | 464 | 0.63 | 0.77 | 39 | empty |
Interfaces
18 interfaces between chains.
- E–H · 4359 Ų buried · 21 hydrogen bonds · protein-protein
- G–F · 4294 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 3574 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 3564 Ų buried · 27 hydrogen bonds · protein-protein
- B–F · 1731 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3O4X · Crystal structure of complex between amino and carboxy terminal fragments of mDia1 · the same entry in another collection · chain F against F, 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 0.83
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 3O4X · PDBe 3O4X · UniProt O08808
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