MolNFT v1 · #123206 · protein
RAB11 bound to myova-gtd
5JCZ · RAS-related protein rab-11A: “RAB11 bound to myova-gtd”. X-ray diffraction, 3 ligands (GDP, BEF, MG), 20 pockets (best druggability 0.76). MolNFT v1 #123206 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5JCZ
- Type
- protein
- Length
- 1,581 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-11A; Unconventional myosin-va
- UniProt
- P62491, Q9Y4I1
- Ligands
- GDP, BEF, MG
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 55% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein rab-11A | protein | 172 | 37% helix, 27% strand | P62491 |
| B | Unconventional myosin-va | protein | 364 | 62% helix, 1% strand | Q9Y4I1 |
| C | Unconventional myosin-va | protein | 364 | 64% helix, 1% strand | Q9Y4I1 |
| D | RAS-related protein rab-11A | protein | 173 | 36% helix, 27% strand | P62491 |
| E | Unconventional myosin-va | protein | 361 | 64% helix, 1% strand | Q9Y4I1 |
| I | RAS-related protein rab-11A | protein | 147 | 35% helix, 22% strand | P62491 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 3 copies · chains A, D, I
- BEF · Beryllium trifluoride ion · ligand · 3 copies · chains A, D, I
- MG · Magnesium ion · metal · 4 copies · chains A, C, E, D, I
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, C, B, D, E
- ACT · Acetate ion · additive · 2 copies · chains A, C
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 768 | 0.76 | 0.80 | 83 | empty |
| 2 | 189 | 0.65 | 0.84 | 32 | empty |
| 3 | 516 | 0.63 | 0.76 | 47 | empty |
| 4 | 483 | 0.63 | 0.76 | 43 | EDO, GOL |
| 5 | 172 | 0.61 | 0.83 | 28 | EDO |
Interfaces
7 interfaces between chains.
- C–E · 970 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 862 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 854 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 587 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 566 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5JCZ · Rab11 bound to MyoVa-GTD · the same entry in another collection · chain I against I, TM-score 1.00
- Q9Y4I1 · AlphaFold monomer V2.0 prediction for unconventional myosin-va (Q9Y4I1) · a predicted model of the same protein · chain E against A, TM-score 0.98
- P62491 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-11A (P62491) · a predicted model of the same protein · chain I against A, TM-score 0.97
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 Q9Y4I1
- Elsewhere: RCSB PDB 5JCZ · PDBe 5JCZ · UniProt P62491 · UniProt Q9Y4I1
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