MolNFT v1 · #62460 · protein
Crystal structure of MDIA1-tsh gbd-FH3 in complex with CDC42-gmppnp
3EG5 · Cell division control protein 42 homolog: “Crystal structure of MDIA1-tsh gbd-FH3 in complex with CDC42-gmppnp”. X-ray diffraction, 2 ligands (GNP, MG), 14 pockets (best druggability 0.71). MolNFT v1 #62460 on GenesisL1: 3D…
- PDB
- 3EG5
- Type
- protein
- Length
- 1,030 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division control protein 42 homolog; Protein diaphanous homolog 1
- UniProt
- P60766, O08808
- Ligands
- GNP, MG
- Pockets
- 14 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 62% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cell division control protein 42 homolog | protein | 178 | 39% helix, 24% strand | P60766 |
| B, D | Protein diaphanous homolog 1 | protein | 337 | 74% helix, 0% strand | O08808 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 460 | 0.71 | 0.81 | 28 | empty |
| 2 | 496 | 0.63 | 0.76 | 65 | empty |
| 3 | 384 | 0.61 | 0.77 | 39 | empty |
| 4 | 61 | 0.52 | 0.86 | 14 | empty |
| 5 | 62 | 0.52 | 0.86 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–D · 3431 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1076 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1074 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3EG5 · Crystal structure of MDIA1-TSH GBD-FH3 in complex with CDC42-GMPPNP · the same entry in another collection · chain D against D, TM-score 1.00
- P60766 · AlphaFold monomer V2.0 prediction for cell division control protein 42 homolog (P60766) · a predicted model of the same protein · chain C against A, TM-score 0.98
- O08808 · AlphaFold monomer V2.0 prediction for protein diaphanous homolog 1 (O08808) · a predicted model of the same protein · chain B 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 P60766
- Every structure of UniProt O08808
- Elsewhere: RCSB PDB 3EG5 · PDBe 3EG5 · UniProt P60766 · UniProt O08808
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