MolNFT v1 · #164299 · protein
Human RAB8A phosphorylated at SER111 in complex with GDP
6STF · RAS-related protein rab-8A: “Human RAB8A phosphorylated at SER111 in complex with GDP”. X-ray diffraction, 2 ligands (GDP, MG), 11 pockets (best druggability 0.73). MolNFT v1 #164299 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6STF
- Type
- protein
- Length
- 825 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-8A
- UniProt
- P61006
- Ligands
- GDP, MG
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 36% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein rab-8A | protein | 174 | 36% helix, 25% strand | P61006 |
| B | RAS-related protein rab-8A | protein | 167 | 37% helix, 26% strand | P61006 |
| C | RAS-related protein rab-8A | protein | 166 | 34% helix, 28% strand | P61006 |
| D | RAS-related protein rab-8A | protein | 158 | 35% helix, 28% strand | P61006 |
| E | RAS-related protein rab-8A | protein | 160 | 36% helix, 30% strand | P61006 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 5 copies · chains A, B, C, D, E
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 497 | 0.73 | 0.82 | 45 | empty |
| 2 | 741 | 0.67 | 0.75 | 50 | empty |
| 3 | 329 | 0.65 | 0.80 | 40 | GDP, MG |
| 4 | 295 | 0.64 | 0.81 | 43 | GDP, MG |
| 5 | 224 | 0.53 | 0.76 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–E · 766 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 511 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 482 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 409 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 406 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (phosphorylation).
Compared structures
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 P61006
- Elsewhere: RCSB PDB 6STF · PDBe 6STF · UniProt P61006
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