Research workbench
Crystal structure of full length centaurin alpha-1 bound with the fha domain of KIF13B (capri target)
Analyse Crystal structure of full length centaurin alpha-1 bound with the fha domain of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FM8
- Type
- protein
- Length
- 910 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kinesin-like protein KIF13B; Centaurin-alpha-1
- UniProt
- Q9NQT8, O75689
- Ligands
- ZN, UNX, SO4
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kinesin-like protein KIF13B | protein | 98 | 0% helix, 43% strand | Q9NQT8 |
| B | Kinesin-like protein KIF13B | protein | 95 | 0% helix, 41% strand | Q9NQT8 |
| C | Centaurin-alpha-1 | protein | 364 | 32% helix, 27% strand | O75689 |
| D | Centaurin-alpha-1 | protein | 353 | 30% helix, 27% strand | O75689 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains C, D
- UNX · Unknown atom or ion · ion · 22 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 3 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1130 | 0.84 | 0.84 | 109 | UNX, SO4 |
| 2 | 416 | 0.66 | 0.79 | 31 | empty |
| 3 | 369 | 0.60 | 0.76 | 31 | UNX |
| 4 | 212 | 0.46 | 0.74 | 35 | UNX |
| 5 | 189 | 0.45 | 0.74 | 34 | empty |
Interfaces
5 interfaces between chains.
- C–D · 767 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 678 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 675 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 270 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 264 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3FM8 · Crystal structure of full length centaurin alpha-1 bound with the FHA domain of KIF13B… · the same entry in another collection · chain D against D, TM-score 1.00
- O75689 · AlphaFold monomer V2.0 prediction for arf-gap with dual pH domain- containing protein 1… · a predicted model of the same protein · chain D against A, TM-score 0.97
- Q9NQT8 · AlphaFold monomer V2.0 prediction for kinesin-like protein KIF13B (Q9NQT8) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 Q9NQT8
- Every structure of UniProt O75689
- Elsewhere: RCSB PDB 3FM8 · PDBe 3FM8 · UniProt Q9NQT8 · UniProt O75689
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