Research workbench
Structure of RAB8 in complex with MSS4
Analyse Structure of RAB8 in complex with MSS4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FU5
- Type
- protein
- Length
- 517 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide exchange factor MSS4; RAS-related protein rab-8A
- UniProt
- P47224, P55258
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.49
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Guanine nucleotide exchange factor MSS4 | protein | 107 | 6% helix, 40% strand | P47224 |
| C | RAS-related protein rab-8A | protein | 146 | 36% helix, 31% strand | P55258 |
| D | RAS-related protein rab-8A | protein | 157 | 37% helix, 29% strand | P55258 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.49 | 0.75 | 31 | empty |
| 2 | 163 | 0.47 | 0.76 | 28 | empty |
| 3 | 51 | 0.43 | 0.84 | 16 | empty |
| 4 | 128 | 0.41 | 0.75 | 21 | empty |
| 5 | 73 | 0.31 | 0.74 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1145 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 989 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 689 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct).
Compared structures
- 2FU5 · structure of Rab8 in complex with MSS4 · the same entry in another collection · chain A against A, TM-score 1.00
- P47224 · AlphaFold monomer V2.0 prediction for guanine nucleotide exchange factor MSS4 (P47224) · a predicted model of the same protein · chain A against A, TM-score 0.96
- P55258 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-8A (P55258) · a predicted model of the same protein · chain C against A, TM-score 0.88
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 P47224
- Every structure of UniProt P55258
- Elsewhere: RCSB PDB 2FU5 · PDBe 2FU5 · UniProt P47224 · UniProt P55258
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