Research workbench
RAB6A:KIF20A complex
Analyse RAB6A:KIF20A complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LEF
- Type
- protein
- Length
- 421 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-6A; Kinesin-like protein KIF20A
- UniProt
- P20340, P97329
- Ligands
- GTP, MG, SO4
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein rab-6A | protein | 166 | 37% helix, 28% strand | P20340 |
| B | RAS-related protein rab-6A | protein | 159 | 40% helix, 24% strand | P20340 |
| C | Kinesin-like protein KIF20A | protein | 49 | 90% helix, 0% strand | P97329 |
| D | Kinesin-like protein KIF20A | protein | 47 | 94% helix, 0% strand | P97329 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · chains A
- IPA · Isopropyl alcohol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 331 | 0.61 | 0.78 | 54 | GTP, MG, IPA |
| 2 | 296 | 0.58 | 0.77 | 44 | GTP, MG |
| 3 | 130 | 0.39 | 0.74 | 20 | empty |
| 4 | 50 | 0.35 | 0.79 | 15 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1301 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 507 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 460 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 390 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 259 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5LEF · Rab6A:Kif20A complex · the same entry in another collection · chain D against D, TM-score 1.00
- P20340 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-6A (P20340) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P97329 · AlphaFold monomer V2.0 prediction for kinesin-like protein KIF20A (P97329) · a predicted model of the same protein · chain D against A, TM-score 0.86
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 P20340
- Every structure of UniProt P97329
- Elsewhere: RCSB PDB 5LEF · PDBe 5LEF · UniProt P20340 · UniProt P97329
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