Research workbench
The crystal structure of ARF6-MKLP1 (mitotic kinesin-like protein 1) complex
Analyse The crystal structure of ARF6-MKLP1 (mitotic kinesin-like protein 1) complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VHX
- Type
- protein
- Length
- 1,050 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosylation factor 6; Kinesin-like protein KIF23
- UniProt
- P62331, Q02241
- Ligands
- GTP, MG
- Pockets
- 13 · best druggability 0.48
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | ADP-ribosylation factor 6 | protein | 162 | 30% helix, 28% strand | P62331 |
| B, D | Kinesin-like protein KIF23 | protein | 106 | 6% helix, 43% strand | Q02241 |
| F | Kinesin-like protein KIF23 | protein | 102 | 6% helix, 47% strand | Q02241 |
| H | Kinesin-like protein KIF23 | protein | 88 | 7% helix, 52% strand | Q02241 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains A, C, E, G
- MG · Magnesium ion · metal · 4 copies · chains A, C, E, G
- GOL · Glycerol · additive · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.48 | 0.81 | 24 | GTP, MG |
| 2 | 94 | 0.47 | 0.81 | 24 | GTP, MG |
| 3 | 100 | 0.47 | 0.80 | 24 | GTP, MG |
| 4 | 72 | 0.47 | 0.83 | 21 | empty |
| 5 | 96 | 0.46 | 0.80 | 23 | GTP, MG |
Interfaces
10 interfaces between chains.
- C–D · 1177 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1171 Ų buried · 24 hydrogen bonds · protein-protein
- F–H · 1096 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 1068 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 998 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3VHX · The crystal structure of Arf6-MKLP1 (Mitotic kinesin-like protein 1) complex · the same entry in another collection · chain H against H, TM-score 1.00
- P62331 · AlphaFold monomer V2.0 prediction for ADP-ribosylation factor 6 (P62331) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P62331
- Every structure of UniProt Q02241
- Elsewhere: RCSB PDB 3VHX · PDBe 3VHX · UniProt P62331 · UniProt Q02241
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