Research workbench
Structure of the cancer associated RAB25 protein in complex with FIP2
Analyse Structure of the cancer associated RAB25 protein in complex with FIP2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TSO
- Type
- protein
- Length
- 444 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-25; RAB11 family-interacting protein 2
- UniProt
- P57735, Q7L804
- Ligands
- GNP, MG, PO4
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein rab-25 | protein | 169 | 37% helix, 27% strand | P57735 |
| B | RAS-related protein rab-25 | protein | 167 | 35% helix, 27% strand | P57735 |
| C, D | RAB11 family-interacting protein 2 | protein | 54 | 80% helix, 2% strand | Q7L804 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 5 copies · chains A, C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 376 | 0.60 | 0.77 | 44 | MG, GNP |
| 2 | 61 | 0.45 | 0.83 | 13 | GOL |
| 3 | 120 | 0.44 | 0.78 | 27 | MG, GNP |
| 4 | 161 | 0.43 | 0.75 | 27 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1527 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 695 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 690 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 227 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 212 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3TSO · Structure of the cancer associated Rab25 protein in complex with FIP2 · the same entry in another collection · chain A against A, TM-score 1.00
- P57735 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-25 (P57735) · a predicted model of the same protein · chain B against A, TM-score 0.97
- Q7L804 · AlphaFold monomer V2.0 prediction for RAB11 family-interacting protein 2 (Q7L804) · a predicted model of the same protein · chain C against A, TM-score 0.84
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 P57735
- Every structure of UniProt Q7L804
- Elsewhere: RCSB PDB 3TSO · PDBe 3TSO · UniProt P57735 · UniProt Q7L804
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