Research workbench
Crystal structure of MYO5B globular tail domain in complex with active RAB11A
Analyse Crystal structure of MYO5B globular tail domain in complex with active RAB11A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LX0
- Type
- protein
- Length
- 1,104 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-11A; Unconventional myosin-vb
- UniProt
- P62491, Q9ULV0
- Ligands
- BEF, GDP, MG
- Pockets
- 12 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 55% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | RAS-related protein rab-11A | protein | 171 | 36% helix, 27% strand | P62491 |
| B | Unconventional myosin-vb | protein | 382 | 60% helix, 1% strand | Q9ULV0 |
| D | Unconventional myosin-vb | protein | 380 | 59% helix, 2% strand | Q9ULV0 |
Ligands and binding sites
- BEF · Beryllium trifluoride ion · ligand · 2 copies · chains A, C
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains A, C
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 315 | 0.60 | 0.78 | 35 | empty |
| 2 | 301 | 0.59 | 0.78 | 33 | empty |
| 3 | 220 | 0.56 | 0.79 | 30 | empty |
| 4 | 244 | 0.55 | 0.78 | 36 | empty |
| 5 | 151 | 0.52 | 0.80 | 29 | MG, BEF, GDP |
Interfaces
5 interfaces between chains.
- A–B · 1037 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 964 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 553 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 525 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 30 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4LX0 · Crystal structure of Myo5b globular tail domain in complex with active Rab11a · the same entry in another collection · chain A against A, TM-score 1.00
- P62491 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-11A (P62491) · a predicted model of the same protein · chain A against A, TM-score 0.97
- Q9ULV0 · AlphaFold monomer V2.0 prediction for unconventional myosin-vb (Q9ULV0) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 P62491
- Every structure of UniProt Q9ULV0
- Elsewhere: RCSB PDB 4LX0 · PDBe 4LX0 · UniProt P62491 · UniProt Q9ULV0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.