MolNFT v1 · #99220 · protein
Crystal structure of MYO5B globular tail domain in complex with active RAB11A
4LX0 · RAS-related protein rab-11A: “Crystal structure of MYO5B globular tail domain in complex with active RAB11A”. X-ray diffraction, 3 ligands (BEF, GDP, MG), 12 pockets (best druggability 0.60). MolNFT v1 #99220 on GenesisL1: 3D…
- 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
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